Core/shell structure platform for immunotherapy

ABSTRACT

Disclosed are biocompatible core/shell compositions suitable for the delivery of populations of mRNA molecules to mammalian cells. The disclosed core-shell structured multicomponent compositions are optimized for the delivery of mRNAs encoding one or more cancer- or tumor-specific antigens to a population of antigen presenting cells, including, for example, human dendritic cells, macrophages and B cells. Also disclosed are methods for use of these compositions as therapeutic cancer vaccines.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application claims priority to PCT Int. Pat. Appl. No.PCT/US2018/015601, and to U.S. Provisional Pat. Appl. No. 62/451,575,filed Jan. 27, 2017, the contents of each of which is specificallyincorporated herein in its entirety by express reference thereto.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under grant numberCA193880 awarded by the National Institutes of Health and grant numberW81XWH-12-1-0414 awarded by the United States Army Medical Research andMaterial Command. The government has certain rights in the invention.

SEQUENCE LISTING

The present application is being filed along with a sequence listing inelectronic format. The sequence listing is provided as a file entitled,“37182-215US01_ST25.txt”, created on Jan. 26, 2018 which is 1743 bytesin size. The information in the electronic format of the sequencelisting is incorporated herein by reference in its entirety.

NAMES OF THE PARTIES TO A JOINT RESEARCH AGREEMENT

Not Applicable.

BACKGROUND OF THE INVENTION Field of the Invention

The present disclosure relates to the fields of molecular biology,oncology and in particular, multi-component compositions optimized formRNA vaccines. Formulations and medicaments including these compositionsare also disclosed, as well as methods for efficient delivery ofmRNA-based vaccines to mammalian cells, and for treating and/orameliorating the symptoms of one or more cancers or tumors in anaffected mammal.

Description of Related Art

Therapeutic Vaccines

A vaccine is usually composed of antigens that can be recognized by thebody's immune system and one or more adjuvants that can boost the body'simmune reaction. A therapeutic cancer vaccine, however, is totallydifferent from the prophylactic vaccines used to prevent infectiousdiseases, as the vaccine must be potent enough to generate cancercell-killing immune cells instead of producing pathogen-fightingantibodies. Therapeutic vaccines have a huge potential in the treatmentof multiple types of life-threatening diseases including cancer andinfectious diseases. A key issue to determine success of cancervaccination is potent induction of anti-tumor responses against theantigen of choice. Both protein peptides and DNA plasmids havetraditionally served as antigens for vaccine development (Melero et al.,2014; Schwartzentruber et al., 2011; Kantoff et al., 2010). Proteins andpeptides are relatively easy to prepare and can be produced in largescale; however, the choice of antigen peptide is dependent on thepatient's unique type of major histocompatibility complex (MEW)proteins, and thus needs to be customized to match with individualpatients. On the other hand, DNA vaccines suffer from low potency andrun the risk of uncontrolled genomic integration (McNamara et al.,2015).

mRNA-Based Cancer Vaccines

mRNA has recently emerged as an ideal antigen source for therapeuticcancer vaccines (Sullenger and Nair, 2016). mRNA molecules can betailored to encode multiple antigens, and serve as an adjuvant bytriggering Toll-like receptor (TLR) signaling in the antigen-presentingcells (Heil et al., 2004; Diebold et al., 2004). In addition,mRNA-mediated gene transfer can occur in non-dividing cells sincenuclear translocation and transcription is not required, while plasmidDNA-mediated gene transfer is mostly effective in dividing cells(McNamara et al., 2015; Kallen and Thess, 2014).

Since the negatively-charged mRNA molecules cannot enterantigen-presenting cells directly, mRNA-based vaccine is usuallyprepared by transfecting mRNA molecules into patient-derived dendriticcells (DCs) by electroporation (Van Tendeloo et al., 2001). The DCvaccine is then reintroduced back to the patient for tumor antigensynthesis, processing and presentation. A number of DC vaccines havereached different stages of clinical trials (Wilgenhof et al., 2013).However, this procedure does not allow mass production of off-the-shelftherapeutic vaccines.

An alternative approach to prepare the mRNA vaccine is to package mRNAmolecules in nanoparticles and directly inoculate them into the bodywhere the vaccine is taken up by the antigen-presenting cells. Thisapproach takes advantage of the high phagocytic capacity ofantigen-presenting cells. The protamine-condensed mRNA vaccines comprisean important part in this group, and several of them are at differentstages of preclinical studies and clinical trials (Weide et al., 2009).Packaging mRNA with protamine not only enables cellular uptake ofvaccine particles, but also facilitates stimulation of MyD88-dependentTLR-7/8 signaling in the host cells (Scheel et al., 2005). However, mRNAdegradation is a potential concern, as part of the naked mRNA is exposedto the body fluid and is vulnerable to attack by plasma and tissueRNases. In addition, exposure of the mRNA molecules tonon-antigen-presenting cells runs the risk of triggering adversereactions inside the body.

Deficiencies in the Prior Art

Industry and academia have labored for a long time to develop effectivetherapeutic cancer vaccines but little success has been achieved so far.One type of therapeutic cancer vaccine that is being tested inpreclinical and clinical studies is an mRNA vaccine, which is comprisedof an mRNA molecule that is condensed in a core structure (ranging from˜20 nanometers to a few hundred nanometers). Once the mRNA vaccine istaken up by antigen-presenting cells, the mRNA is released inside thosecells, and then used as templates to produce the encoded antigen(s). Anexample of such vaccine is the CuraVac mRNA vaccine.

Major problems with such vaccines are: 1) the mRNA molecules are exposedto body fluids, and are thus vulnerable to degradation by tissue,cellular, and/or plasma enzymes; 2) the “naked” mRNA molecules caninteract with all types of immune cells, which can lead to unwanted sideeffects (such as secreting high levels of cytokines); and 3) such mRNAsare not very effectively internalized by antigen-presenting cells.

Tumor-associated neoantigens are constantly being identified as a resultof the massive cancer genome sequencing effort and technology advance inpredicting immunogenic tumor mutations (see e.g., Schumacher andSchreiber, 2015; Shukla et al., 2015; Yadav et al., 2014). This resourcehas provided an unprecedented opportunity for developing new andimproved cancer vaccines. Unfortunately, development of the enablingtechnology for cancer vaccines has lagged.

However, immunotherapies such as those disclosed herein, represent a newavenue for cancer therapeutics. These therapeutics may be based on theunique genetic features of particular cancer cells, thus sparing thebody from unnecessary attack by conventional standard-of-carechemotherapy drugs. The mRNA-based vaccines disclosed herein have theflexibility to include multiple neoantigens within the same construct,and the choice(s) of antigen peptide(s) can be tailored based on theunique mutational spectrum of the individual patient, making precisionor “personalized” medicine possible.

BRIEF SUMMARY OF THE INVENTION

The biocompatible, shell/core multicomponent vaccine delivery platformdescribed herein represents an important advance in overcoming these andother inherent limitations in the art by providing, in a general sense,compositions for effective delivery of mRNAs to, and efficient uptakeby, antigen presenting cells (such as dendritic cells) in methods forstimulating anti-cancer immunity.

In an overall and general sense, the disclosed core/shell compositionscan efficiently deliver nucleic acid molecules (including, for example,mRNAs encoding one or more cancer- or tumor-specific antigens) packagedwithin a “core” structure, and encapsulated with an outer hydrophiliclipid bilayer-containing “shell,” to one or more selected mammaliancells (including, for example, one or more antigen-presenting cells,such as dendritic cells, macrophages, and B cells, without limitation.The presence of the lipophilic shell encapsulating the inner hydrophobiccore protects the nucleic acids from degradation by tissue enzymes orinteraction with other immune cells. Moreover, the lipophilic shell alsoaffords increased internalization of the compositions by theantigen-presenting cells, and stimulates more potent anti-tumoralimmunity when compared to conventional mRNA-based therapeutic vaccines.

In an important advancement over existing technology, the disclosedcore/shell multicomponent vaccine delivery systems permit an alternativeto the current “bottleneck” in mRNA-based cancer vaccine development bystimulating a robust anti-tumoral immunity, that is superior toconventional, single-component “core+nucleic acids-only” structures thatmake up existing mRNA-based vaccines. These multi-component,hydrophilic/hydrophobic shell/cores facilitate preparation of mRNAvaccines that are significantly more potent than conventional mRNAvaccines in stimulating dendritic cell maturation, and thus, antigenprocessing and presentation.

In particular embodiments, the present disclosure provides core-shellstructured mRNA vaccines that are significantly more potent thanconventional mRNA-core vaccines in stimulating interferon-β,interferon-α, and interleukin-12. Such multicomponent mRNA-based, tumorantigen-encoding therapeutic vaccines find particular use in thepreparation of medicaments for treatment of one or more diseases in amammal, and particularly for the treatment and/or amelioration of one ormore symptoms of a mammalian cancer.

A composition comprising a therapeutic cancer vaccine that comprises apopulation of mRNA molecules that encode at least a first tumor antigen,wherein the population is comprised within a plurality of polyplex coreparticles comprising at least a first positively-charged polymer, andfurther wherein the plurality of polyplex core particles are themselvesencapsulated in a first biocompatible lipid bilayer shell.

Preferably, the first biocompatible lipid bilayer shell facilitatesmacropinocytosis of the plurality of polyplex core particles by one ormore mammalian antigen-presenting cells including human dendritic cells,human macrophages, and human B cells, without limitation.

Such compositions may also further optionally include one or moreadjuvants, such as CpG, poly(I:C), alum, cyclic GMP-AMP (cGAMP),lipopolysaccharide (LPS), monophosphoryl lipid A (MPLA), or anycombination thereof, encapsulated within the biocompatible lipidbilayer, contained within the mRNA core, or contained within the spacebetween the core particles and the enveloping hydrophilic phospholipidbilayers surrounding/encompassing them.

In certain embodiments, the positively-charged agent used to prepare thecore particles will include one or more of protamine, polyethyleneimine,poly-(B-amino ester), poly-arginine, poly-lysine, and combinationsthereof.

Similarly, the biocompatible phospholipids used to prepare thehydrophilic shell component will preferably include one or more of1,2-dioleoyl-sn-glycero-3-ethylphosphocholine (EDOPC);1,2-dioleoyl-sn-glycero-3-phosphatidyl-ethanolamine (DOPE);1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethyleneglycol)-2000] (DSPE-PEG); 1,2-dipalmitoyl-sn-glycero-3-phosphocholine(DPPC), 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine (DPPE),O-ethylphosphatidyl choline (EDPPC), cholesterol, and combinationsthereof.

In certain embodiments, the biocompatible phospholipid bilayer willpreferably include:

(a) from about 30% to about 70% of1,2-dioleoyl-sn-glycero-3-ethylphosphocholine (“EDOPC”);

(b) from about 70% to about 30% of1,2-dioleoyl-sn-glycero-3-phosphatidyl-ethanolamine (“DOPE”); or

(c) from about 0.5 to about 5% of1,2-distearoyl-sn-glycero-3-phosphoethanol amine-N-[amino(polyethyleneglycol)-2000](“DSPE-PEG”).

Alternatively, the biocompatible lipid bilayer may preferably include:

(a) from about 45% to about 55% of EDOPC;

(b) from about 55% to about 45% of DOPE; and

(c) from about 1% to about 2% of DSPE-PEG.

In the practice of the invention, the compositions disclosed herein willpreferably include a population of nucleic acid molecules, such as mRNA,that encode at least one antigen, which is specific for one or moremammalian cancer or tumor cells. Exemplary cancer cell-specific antigensinclude, but are not limited to tumor-associated antigens such as breastcancer-specific HER2 antigens E75 and p66, melanoma-specific antigenTRP2, and tumor mutated antigens [neoantigens] such as HER2 with YVMAinsertion in exon 20 [HER2^(YVMA)] in breast and lung cancers, and thosegenerated as a result of mutations in the cancer genome. Exemplarycancer- and tumor-specific antigens include, but are not limited to:HER2E75, HER2p66, HER2^(YVMA), and TRP2.

The compositions disclosed herein are preferably suitable for increasingthe level of type I interferon (IFN-I) expression, when introduced intosuitable mammalian cells; and preferably suitable for increasing theexpression of one or more of IFN-α4, IFN-β, and their down-streamcytokines such as CCL-5, for example.

In certain embodiments, the disclosed compositions will be suitable forintroduction into a population of one or more types of mammalian cells.Such cells include, but are not limited to, dendritic cells,macrophages, B cells, cancer cells, or a combination thereof.

The compositions disclosed herein may further optionally include one ormore additional therapeutic agents, including, for example, and withoutlimitation, an agent such as an immunomodulating agent, anantineoplastic agent, a neuroactive agent, a cytotoxic agent, acytostatic agent, an anti-inflammatory agent, an anti-lipidemic agent, ahormone, a receptor agonist, a receptor antagonist, an anti-infectiveagent, a protein, a peptide an antibody, an antigen-binding fragment, anenzyme, an RNA, a DNA, an siRNA, an mRNA, a ribozyme, a hormone, acofactor, a steroid, an antisense molecule, or any combination thereof.In preferred embodiments, the immunomodulating agent is a compoundselected from the group consisting of an IL-12p70, protein, an FLT3ligand [FLT3L], and a small molecule inhibitor of indoleamine2,3-dioxygenase [IDO-1] such as GDC-0919 or INCB24360.

In certain embodiments, the therapeutic agent may include (but notlimited to) one or more compounds such as cyclophosphamide, doxorubicin,5-fluorouracil, docetaxel, paclitaxel, trastuzumab, methotrexate,epirubicin, carboplatin, vinorelbine, capecitabine, gemcitabine,mitoxantrone, isabepilone, eribulin, lapatinib, carmustine, a nitrogenmustard, a sulfur mustard, a platin tetranitrate (e.g., cis-platin),vinblastine, etoposide, camptothecin, or any combination thereof.

In other embodiments, the composition may further optionally include oneor more antigens, antigenic polypeptides, or antigenic peptide fragmentsthereof, including, for example, multiple antigenic peptides that areproduced by the cells separately [i.e., from different mRNA molecules]or together [i.e., from one mRNA molecule]. Such antigens may besoluble, in which they may be incorporated into the lumen or volume asdefined by the exterior of the core, and the inner surface of theexterior lipid bilayer, or in the case of insoluble antigens, may beincorporated within the core structure, and/or within the lipid bilayeritself.

Examples of soluble antigens include, but are not limited to, the p66HER2 antigen peptide (HER2p66), and homologs or antigenic fragmentsthereof.

Examples of slightly soluble antigens include, but are not limited to,the E75 HER2 antigen peptide (HER2E75), and homologs or antigenicfragments thereof.

In certain embodiments, the cancer vaccine delivery compositionsdisclosed herein may be admixed with one or morepharmaceutically-acceptable carriers, buffers, diluents, vehicles, orexcipients, or admixed with one or more surfactants, liposomes,niosomes, ethosomes, transferosomes, phospholipids, sphingosomes,exosomes, or other types of vesicles that are produced by the cellsthemselves.

Such compositions are preferably formulated for systemic administrationto a mammal, and preferably, for intradermal or intravenousadministration, intra-muscular, intraperitoneal, intra-nodal, orintra-ocular administration, or, alternatively, in the form of a skinpatch to a human, and particularly formulated for contacting with, anduptake by, one or more antigen-presenting cells, including, withoutlimitation, human dendritic cells, macrophages, and B cells.

In certain embodiments, the disclosed mRNA-based vaccine compositionsmay be adapted and configured as part of a therapeutic kit that includesthe composition, and at least a first set of instructions foradministration of the composition to a mammal, such as a human cancerpatient, in need thereof. Such kits may be utilized as part of a regimenfor the prevention, diagnosis, treatment, or amelioration of one or moresymptoms of a cancer a hyperproliferative disorder, or other disease,dysfunction, injury, or abnormal condition in the mammal, including,without limitation, infectious diseases [e.g., vaccines for West Nilevirus and Chagas], cardiovascular diseases [e.g., HSP60 vaccine toprevent heart failure], and the like.

A further aspect of the present disclosure is a method for treating orameliorating one or more symptoms of cancer in an animal in needthereof. In an overall and general sense, such a method generallyincludes at least the step of administering to the animal an effectiveamount of one or more of the mRNA-based therapeutic cancer vaccinecompositions disclosed herein, for a time sufficient to treat orameliorate the one or more symptoms of the cancer in the animal. In someembodiments, the cancer may be diagnosed as, or identified as, arefractory, a metastatic, a relapsed, or a treatment-resistant cancer.

Examples of such cancers include, but are not limited to, breast cancer,lung cancer, colorectal cancer, gastric cancer, pancreatic cancer,glioblastoma, head and neck cancer, leukemia, lymphoma, multiplemyeloma, liver cancer, kidney cancer, bladder cancer, melanoma, andrelated conditions in an affected mammal.

In certain embodiments, the cancer may be a metastatic cancer, such asmetastatic breast cancer, metastatic lung cancer, metastatic melanoma,or metastatic colorectal cancer, gastric cancer, pancreatic cancer,glioblastoma, head and neck cancer, liver cancer, kidney cancer, bladdercancer, or one or more related conditions in the affected mammal.

Such methods may further optionally include a step of administering atherapeutically-effective amount of radiation or an additionalchemotherapeutic to the animal, either in a single administration, or ina series of multiple administrations over a period of from one or moredays, over a period of one or more weeks, or over a period of one ormore months or longer.

Such a method may also further optionally include a step ofadministering a second distinct chemotherapeutic agent, or a seconddistinct therapeutic cancer vaccine to the affected mammal undertreatment.

In another embodiment, the present disclosure also provides a method foradministering an active agent, and particularly one or more anti-cancerantigens, or one or more mRNAs that encode such anti-cancer antigens, toone or more cells, tissues, organs, or systems of a mammalian subject inneed thereof. The method generally involves providing to a mammaliansubject in need thereof, one or more of the compositions disclosedherein in an amount and for a time effective to administer the mRNAvaccines to a population of cells (e.g., antigen presenting cells suchas dendritic cells) present in one or more selected tissues, organs,systems, or cells within or about the body of the subject. Inparticularly preferred embodiments, the subject is a human, and thecomposition comprises an mRNA antigen-encoding component containedwithin a population of polyplex core particles, that are themselvescontained within an outer lipid bilayer.

The disclosed compositions find particular utility in a variety of invitro, ex vivo, and in vivo treatment regimens, and they may beformulated alone, or, alternatively, in combination with one or moreadditional agents, including, without limitation, one or moreanti-cancer antigen(s), one or more antigenic peptides, one or morediagnostic reagents, one or more therapeutic reagents, one or morecytotoxic reagents, one or more chemotherapy agents, one or moreadjuvants, one or more immunostimulatory agents, one or moreimmunomodulatory agents, or any combination thereof, for use in avariety of therapeutic indications, including, without limitation, forthe treatment or amelioration of symptoms of one or more human cancers,hyperproliferative disorders, infectious disease, heart disease, and thelike.

As described herein the disclosed vaccine systems may further optionallyinclude one or more active agents, such as, for example, one or moreprophylactic agents, one or more therapeutic agents, one or morediagnostic agents, one or more vaccines, one or more imaging agents, oneor more radiolabels, one or more adjuvanting agents, one or morechemotherapeutic agents, one or more cytotoxic agents, one or morecheckpoint inhibitor drugs [e.g., anti-PD-1 antibody, anti-PD-L1antibody, anti-CTLA-4 antibody, etc.], or any combination thereof.

In related embodiments, the invention also provides therapeutic and/ortherapeutic kits including one or more of the core/shell-based mRNAvaccine delivery systems disclosed herein, typically in combination withone or more pharmaceutically acceptable carriers, one or more devicesfor administration of the compositions to a subject of interest, as wellas one or more instruction sets for using the composition in thediagnosis, or treatment of a mammalian disease such as cancers and thelike.

The invention also provides in an overall and general sense,compositions and methods for effectively delivering a population of mRNAmolecules to a population of mammalian cells (including, for example,dendritic cells, macrophages, B cells, or tumor cells) within the bodyof a mammal. Such compositions are preferably administered to themammalian subject in an amount and for a time effective to treat orameliorate one or more diseases or abnormal conditions in the subject.In certain embodiments, the subject is at risk for, diagnosed with, orsuspected of having one or more abnormal cell proliferative conditions,including, for example, one or more cancers or other hyperproliferativedisorders.

As noted herein, the compositions of the present disclosure may beadministered to the subject through any one or more conventional methodsfor administration, including, without limitation, intravenously,cutaneously, subcutaneously, or by direct injection to one or more cellsor one or more tissues, organs, or tumors within or about the body ofthe subject.

As further described herein, in certain applications, it may bedesirable to contact a population of cells obtained from a subject exvivo with the vaccine compositions disclosed herein, and then,subsequently, to reintroduce the resulting contacted cells into the bodyof the subject. Such ex vivo therapy is particularly contemplated to beuseful in introducing the disclosed mRNA vaccines to populations ofhuman dendritic cells, allowing the active ingredients to be contactedwith the cells, and then to re-introduce the resulting transformed cellsback into the body of the animal. Preferably, dendritic cells extractedfor use in such ex vivo manipulation will be those of the actual patientundergoing treatment.

In particular embodiments, the mRNA vaccine compositions of the presentinvention may be formulated for pharmaceutical administration, andpreferably for administration to a human. Such compositions may furtherinclude one or more additional therapeutic agents, chemotherapeutics,adjuvants, or a second distinct mRNA vaccine.

The mRNA vaccines disclosed herein may also be used in vitro to expandthe population tumor antigen-specific T cells. An example of theapplication is to co-culture with human patient-derived T cells in orderto expand the population of tumor antigen-specific T cells before theyare infused back to the patient.

Additionally, the disclosed mRNA vaccines may also be used to isolatetumor antigen-specific T cell receptor for T cell engineering. Anexample is the co-culture of mRNA vaccine-containing dendritic cellswith human T cells, and isolating the T cells with a high bindingcapacity therefrom. Once the T cells are isolated, their T cellreceptors can be determined by sequencing, and used to generate TCR-Tcells (another branch of cancer immunotherapy).

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and areincluded to demonstrate certain aspects of the present invention. Thepatent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

For promoting an understanding of the principles of the invention,reference will now be made to the embodiments, or examples, illustratedin the drawings and specific language will be used to describe the same.It will, nevertheless be understood that no limitation of the scope ofthe invention is thereby intended. Any alterations and furthermodifications in the described embodiments, and any further applicationsof the principles of the invention as described herein are contemplatedas would normally occur to one of ordinary skill in the art to which theinvention relates.

The invention may be better understood by reference to the followingdescription taken in conjunction with the accompanying drawings, inwhich like reference numerals identify like elements, and in which:

FIG. 1A, FIG. 1B, FIG. 1C, FIG. 1D, FIG. 1E, FIG. 1F, FIG. 1G, FIG. 1H,FIG. 1I, FIG. 1J, FIG. 1K, and FIG. 1L show the structure andcharacterization of lipopolyplex mRNA vaccine. FIG. 1A is a schematicview of a lipopolyplex-mRNA-based vaccine prepared in accordance withone aspect of the present disclosure. The exemplary vaccine is composedof a polyplex lipophobic “core,” assembled through electrostaticinteraction between the positively-charged PbAE polymer and thenegatively-charged mRNA molecules. The resulting polyplex-mRNA core isthen encapsulated into a hydrophilic lipid bilayer “shell.” FIG. 1Bshows a gel retardation assay on exemplary polyplex-mRNA binding. Thesamples were loaded in the following order: free mRNA, polyplex/mRNAwith 10, 20, 30 and 40 (wt./wt.). FIG. 1C, FIG. 1D, and FIG. 1E showtransmission electron microscopy (TEM) images of empty liposomal shells(FIG. 1C), the polyplex/mRNA core (wt./wt.=20) (FIG. 1D), and thelipopolyplex/mRNA core-shell structure (FIG. 1E). FIG. 1F, FIG. 1G, FIG.1H, FIG. 1I, FIG. 1J, and FIG. 1K illustrate eGFP expression in DC2.4cells treated with mRNA-packaged particles: DC2.4 cells were treatedwith PBS control (FIG. 1F), PbAE/eGFP mRNA core (FIG. 1G),EDOPC/DOPE-packaged PbAE/eGFP mRNA (FIG. 1H), DOTAP/Chol-packagedPbAE/eGFP mRNA (FIG. 1I), CHEMS/DOPE/R8-packaged PbAE/eGFP mRNA (FIG.1J), or protamine/eGFP mRNA core (FIG. 1K), and eGFP expression wasdetected by fluorescence microscopy 24 hrs later. FIG. 1L illustratesDC2.4 viability upon treatment with the various particle types;

FIG. 2 illustrates preferential uptake of an exemplary lipopolyplex/mRNAcore-shell vaccine by a population of mammalian dendritic cells. Flowcytometry analysis was performed on GFP-positive cells after DC2.4,MDA-MB-231 and mDMEC cells that had been incubated withlipopolyplex/eGFP mRNA for 24 hrs prior to cell sorting; Abioluminescent image was used to detect luciferase expression in mice 48hrs after s.c. injection of LPP/Luc. On the left is a control mouse; onthe right is a LPP/Luc-treated mouse.

FIG. 3A, FIG. 3B, FIG. 3C, FIG. 3D, FIG. 3E, FIG. 3F, FIG. 3G, and FIG.3H show the mechanism of cell entry. FIG. 3A-FIG. 3H represent images ofDC2.4 cells treated with LPP/0.5 μg FAM-labeled eGFP mRNA in presence ofmock control (FIG. 3A), amiloride (FIG. 3B), chlorpromazine (FIG. 3C),chloroquine (FIG. 3D), genistein (FIG. 3E), or pimozide (FIG. 3F), FIG.3G shows the Image J analysis of FAM-positive cells, while FIG. 311illustrates the time-dependent uptake of LPP/FAM-labeled eGFP mRNA byDC2.4 cells. Error bars represent the mean±standard deviation oftriplicate experiments;

FIG. 4A, FIG. 4B, and FIG. 4C show the DC stimulation by the LPP/mRNAvaccine. FIG. 4A shows cytokine secretion in BMDCs treated with LPP/OVA(EDOPC/DOPE/DSPE-PEG packaged with OVA mRNA and controls; FIG. 4B showsthe inhibition of IL-12 and IFN-β expression by the TLR7/8 inhibitor,ODN2087; FIG. 4C is a comparison between LPP/OVA mRNA and LPP/OVAprotein on DC stimulation. Error bars represent the mean±standarddeviation of triplicate experiments;

FIG. 5A, FIG. 5B, and FIG. 5C show the stimulation of DC antigencross-presentation by the LPP/mRNA vaccine. FIG. 5A is the flowcytometry analysis of H-2kb-OVA257-264 presentation. FIG. 5B shows thetime-dependent IL-2 secretion by OVA-specific CD4+ and CD8+ T cellsafter co-incubation with post-treated BMDCs. B3Z: OVA-specific CD8+ Tcell; DOBW: OVA-specific CD4+ T cell. FIG. 5C shows the time-dependentIL-2 secretion by OVA-specific CD4+ and CD8+ T cells after co-incubationwith post-treated DC2.4 cells; The figure shows a comparison of IL-2secretion by OVA-specific CD8 T cells after co-incubation with DC2.4cells pretreated with LPP/OVA mRNA or LPP/OVA protein;

FIG. 6A and FIG. 6B show the anti-tumor activity from LPP/OVA in vitroand in vivo. FIG. 6A shows the serum IFN-β levels 3, 6, and 24 hrs afters.c. LPP/OVA mRNA vaccination; FIG. 6B illustrates the inhibition ofB16-OVA melanoma lung metastasis by LPP/OVA mRNA. Treatment schedule(top panel) and representative images of the lungs from post-treatmentmice (middle panel) are shown, and average number of tumor nodules inthe lung is summarized (bottom panel). Data are presented as mean±SEM.There were 5 mice in each group; FIG. 6F shows IFN-γ production by PBMCsfrom mice vaccinated with LPP/TRP2 mRNA; FIG. 6G shows the percentage ofTRP2-specific CD8+ T cells in PBMCs from vaccinated mice;

FIG. 7 shows mRNA molecules were mixed with an increasing amount ofpolymer (PbAE), and samples were separated by electrophoresis in anagarose gel. Unbound mRNA molecules moved to the bottom, and bound mRNAmolecules stayed with the polymer on top. Lane #1: free mRNA, Lanes 2-5:mRNA molecules with increasing amount of polymer;

FIG. 8A and FIG. 8B show the size analysis of untargeted and targetedmRNA vaccine nanoparticles, respectively;

FIG. 9A, FIG. 9B, and FIG. 9C shows transmission electron microscopic(TEM) images of an exemplary empty lipid shell (left), an mRNA core(middle), and a whole mRNA vaccine nanoparticle, respectively, inaccordance with one aspect of the present disclosure;

FIG. 10A, FIG. 10B, FIG. 10C, FIG. 10D, FIG. 10E, and FIG. 10F showDC2.4 dendritic cells were co-incubated with the same amount of EGFP(green fluorescent protein) mRNA either in the mRNA core form (PbAE/mRNAcore or Protamine/mRNA core) or packaged in lipid shells (our mRNAvaccine, DOTAP/cholesterol-encapsulated mRNA, orCHEMS/DOPE/R8-encapsulated mRNA). EGFP expression was monitored under afluorescent microscope 24 hrs later;

FIG. 11 shows DC2.4 cells were incubated with naked mRNA core orpackaged mRNA, and cell viability was determined 24 hrs later;

FIG. 12A and FIG. 12B show Cy5-labeled mRNA was packaged into untargetedor targeted vaccines. The fluorescent vaccine particles were thenincubated with DC2.4 cells for 4 hours. Percentage of cells internalizedwith the fluorescent mRNA vaccine particles (FIG. 12A) and cells withtotal fluorescence (FIG. 12B) were measured;

FIG. 13 illustrates the stimulation of dendritic cell maturation by mRNAvaccine. Bone marrow-derived dendritic cells (BMDCs) were treated withmRNA vaccine or individual components of the vaccine, and secretion ofthe Type I interferon cytokine interferon-β (IFN-β) and dendritic cellmaturation marker IL-12p70 was measured by enzyme-linked immunosorbentassay (ELISA);

FIG. 14 demonstrates the inhibition of mRNA vaccine-mediated dendriticcell stimulation by the TLR7/8 inhibitor ODN2095. BMDCs were treatedwith ovalbumin protein (OVA), the TLR7/8 inhibitor ODN2095, mRNA vaccineexpressing OVA, or a combination of mRNA vaccine and ODN2095, andsecretion of the type I interferon cytokine interferon-0 (IFN-β) anddendritic cell maturation marker IL-12p70 was measured by ELISA;

FIG. 15 shows BMDCs that were treated with PBS negative control,protamine/mRNA core, or OVA-specific mRNA vaccine (mRNA vaccine thatexpresses the OVA protein); flow cytometry was then applied to detectCD11c-positive dendritic cells that also displayed MHCI-OVA epitope;

FIG. 16A shows BMDCs cells and FIG. 16B shows DC2.4 cells treated withOVA mRNA vaccine that were co-incubated with OVA-specific CD4 T cells(DOBW) and CD8 T cells (B3Z) for 24 or 48 hrs. IL-2 expression by the Tcells was then detected and quantitated by ELISA;

FIG. 17 shows OVA mRNA vaccine was co-packaged with the IDO1 inhibitorINCB024360, and applied to treat BMDCs. The BMDCs were then co-incubatedwith OVA-specific T cells, and IL-2 secretion was measured by ELISA;

FIG. 18A and FIG. 18B show C57BL6 mice were treated 3 times with PBS,OVA protein, or OVA mRNA vaccine, and cells (including activated Tcells) from spleens and lymph nodes were isolated and applied to test Tcell stimulation status and tumor cell killing activity. In FIG. 18A,Interferon-γ secretion after the isolated cells were challenged (i.e.,co-incubated) with OTI and OTII OVA-specific antigen peptides. In FIG.18B, co-incubation of isolated T cells with B16-OVA tumor cells, andcell viability was measured;

FIG. 19 shows C57BL6 mice with B16-OVA tumor lung metastasis weretreated 3 times with OVA mRNA vaccine (on days 3, 7, and 10). Mice wereeuthanized on day 18, and tumor nodules in the lung were counted. Theupper timeline shows the treatment schedule. Representative lungs fromthe PBS control group and the OVA mRNA vaccine treatment group are shownin the middle of the image; quantitation, based upon the number of tumornodules in the lung is shown for comparison;

FIG. 20 shows an exemplary schematic of a vaccine structure inaccordance with one particular aspect of the present disclosure. In it,an overview of the mRNA vaccine nanoparticle composed of (1) the mRNAcore in the center, (2) lipid shell on outside (with or withouttargeting moiety), and (3) small molecules and/or proteins in betweencan be visualized; and

FIG. 21 shows co-packaging of mRNA encoding IL12p70 further promotesmRNA vaccine activity as compared to a single antigen vaccine alone.

BRIEF DESCRIPTION OF THE SEQUENCES

SEQ ID NO:1 is an exemplary cytotoxic T cell epitope derived fromwild-type TP53 peptide, and which is useful in accordance with one ormore aspects of the present disclosure;

SEQ ID NO:2 is an exemplary cytotoxic T cell epitope derived frommutated TP53 peptide, and which is useful in accordance with one or moreaspects of the present disclosure;

SEQ ID NO:3 is an exemplary cytotoxic T cell epitope derived fromwild-type TP53 peptide, and which is useful in accordance with one ormore aspects of the present disclosure;

SEQ ID NO:4 is an exemplary cytotoxic T cell epitope derived frommutated TP53 peptide, and which is useful in accordance with one or moreaspects of the present disclosure;

SEQ ID NO:5 is an exemplary cytotoxic T cell epitope derived fromwild-type PIK3CA peptide, and which is useful in accordance with one ormore aspects of the present disclosure;

SEQ ID NO:6 is an exemplary cytotoxic T cell epitope derived frommutated PIK3CA peptide, and which is useful in accordance with one ormore aspects of the present disclosure;

SEQ ID NO:7 is an exemplary cytotoxic T cell epitope derived fromwild-type PIK3CA peptide, and which is useful in accordance with one ormore aspects of the present disclosure;

SEQ ID NO:8 is an exemplary cytotoxic T cell epitope derived frommutated PIK3CA peptide, and which is useful in accordance with one ormore aspects of the present disclosure;

SEQ ID NO:9 is an exemplary cytotoxic T cell epitope derived fromwild-type PTEN peptide, and which is useful in accordance with one ormore aspects of the present disclosure; and

SEQ ID NO:10 is an exemplary cytotoxic T cell epitope derived frommutated PTEN peptide, and which is useful in accordance with one or moreaspects of the present disclosure.

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

Illustrative embodiments of the invention are described below. In theinterest of clarity, not all features of an actual implementation aredescribed in this specification. It will of course be appreciated thatin the development of any such actual embodiment, numerousimplementation-specific decisions must be made to achieve thedevelopers' specific goals, such as compliance with system-related andbusiness-related constraints, which will vary from one implementation toanother. Moreover, it will be appreciated that such a development effortmight be complex and time-consuming, but would be a routine undertakingfor those of ordinary skill in the art having the benefit of thisdisclosure.

Cancer

Cancer is arguably one of the biggest global threats to public health.Cancer metastasis is a key feature of malignancy and contributes to morethan 90% solid tumor-related deaths. Because of poorly understoodmechanisms of cancer metastasis, there is no diagnosis/prognosissignature and specific treatment available to efficiently control tumormetastasis. In fact, metastasis is a complex process involvingwell-coordinated sequence of events where some tumor cells leave theprimary lesion and take residence at distal sites. As not all cells inprimary tumors have the capacity to metastasize, it is reasoned thatmetastatic cancer cells may possess special features that can providevaluable therapeutic targets.

mRNA-Based Therapeutic Cancer Vaccines

mRNA-based therapeutic cancer vaccines have the benefit of triggeringrobust anti-cancer immunity without the potential danger of genomeintegration from DNA vaccines or the limitation of antigen selectionfrom peptide vaccines. Yet, a conventional mRNA vaccine comprised ofcondensed mRNA molecules in a positively-charged protein core structureis not effectively internalized by antigen-presenting cells, and thus,cannot offer sufficient protection to the mRNA molecules fromdegradation by plasma and tissue enzymes.

Lipopolyplex Compositions for Packaging mRNAs

In one aspect, the present disclosure provides lipopolyplex-(LPP) andprotein-based shell/core delivery systems that are designed to packagenucleic acid molecules (including, for example mRNAs), into a polymericpolyplex “core” that is then loaded into “shell” structure that iscomprised of a phospholipid bilayer. An illustrative system is shown inFIG. 1A, and a generalized schematic for such vaccine delivery systemsis shown in FIG. 20. These compositions not only can protect the mRNAmolecules inside the hydrophobic polyplex core structure from attack byRNAses and subsequent degradation, but the presence of envelopingphospholipid bilayer shell structure surrounding the core also serves tomore efficiently internalize the vector by antigen-presenting cells(including, without limitation macrophages, B cell, dendritic cells, andthe like), and facilitate particle transport through the vesicularsystem, and ultimate release of the mRNA molecules from the corestructure into the cytosol to facilitate production of the encodedantigen(s).

In Example 1, the composition and morphology of particular LPPs havebeen systematically characterized, and the cellular uptake of LPP/mRNAby DCs and resulting protein synthesis in the DCs of the encoded peptideantigen has also been studied. By applying ovalbumin (OVA) as an antigenmodel, the immune responses to the LPP/OVA mRNA vaccine were examined incell culture, and anti-tumoral immunity was also evaluated in a murinemodel of melanoma lung metastasis that was established withOVA-expressing B16 melanoma cells.

Pharmaceutical Formulations

In certain embodiments, the present disclosure concerns vaccine deliverycompositions prepared in pharmaceutically-acceptable formulations foradministration to one or more cells or tissues of an animal, eitheralone, or in combination with one or more other modalities of diagnosis,prophylaxis and/or therapy. The formulation of pharmaceuticallyacceptable excipients and carrier solutions is well known to those ofordinary skill in the art, as is the development of suitable dosing andtreatment regimens for using the particular LPP-mRNA-based vaccinecompositions described herein in a variety of diagnostic andcancer-prognostic regimens.

In certain circumstances it will be desirable to deliver the disclosedpolymeric polyplex core/phospholipid bilayer shell-based vaccinedelivery systems in suitably-formulated pharmaceutical vehicles by oneor more standard delivery devices, including, without limitation,subcutaneously, parenterally, intravenously, intramuscularly,intrathecally, intratumorally, intraperitoneally, transdermally,topically, by oral or nasal inhalation, or by direct injection to one ormore cells, tissues, or organs within or about the body of an animal,and preferably a human.

The methods of administration may also include those modalities asdescribed in U.S. Pat. Nos. 5,543,158; 5,641,515, and 5,399,363, each ofwhich is specifically incorporated herein in its entirety by expressreference thereto. Solutions of the active compounds as freebase orpharmacologically acceptable salts may be prepared in sterile water, andmay be suitably mixed with one or more surfactants, such ashydroxypropylcellulose. Dispersions may also be prepared in glycerol,liquid polyethylene glycols, oils, or mixtures thereof. Under ordinaryconditions of storage and use, these preparations contain a preservativeto prevent the growth of microorganisms.

For administration of an injectable aqueous solution, withoutlimitation, the solution may be suitably buffered, if necessary, and theliquid diluent first rendered isotonic with sufficient saline orglucose. These particular aqueous solutions are especially suitable forintravenous, intramuscular, subcutaneous, transdermal, subdermal, and/orintraperitoneal administration. In this regard, the compositions of thepresent invention may be formulated in one or more pharmaceuticallyacceptable vehicles, including for example sterile aqueous media,buffers, diluents, etc. (see, e.g., “REMINGTON'S PHARMACEUTICALSCIENCES” 15th Edition, pp. 1035-1038 and 1570-1580). While somevariation in dosage will necessarily occur depending on the condition ofthe subject being treated, the extent of the treatment, and the site ofadministration, the person responsible for administration willnevertheless be able to determine the correct dosing regimensappropriate for the individual subject using ordinary knowledge in themedical and pharmaceutical arts.

Sterile injectable compositions may be prepared by incorporating thedisclosed vaccine compositions in the required amount in the appropriatesolvent with several of the other ingredients enumerated above, asrequired, followed by filtered sterilization. Generally, dispersions canbe prepared by incorporating the selected sterilized activeingredient(s) into a sterile vehicle that contains the basic dispersionmedium and the required other ingredients from those enumerated above.The vaccine compositions disclosed herein may also be formulated in aneutral or salt form.

Pharmaceutically acceptable salts include the acid addition salts(formed with the free amino groups of the protein), and which are formedwith inorganic acids such as, without limitation, hydrochloric orphosphoric acids, or organic acids such as, without limitation, acetic,oxalic, tartaric, mandelic, and the like. Salts formed with the freecarboxyl groups can also be derived from inorganic bases such as,without limitation, sodium, potassium, ammonium, calcium, or ferrichydroxides, and such organic bases as isopropylamine, trimethylamine,histidine, procaine, and the like. Upon formulation, solutions will beadministered in a manner compatible with the dosage formulation, and insuch amount as is effective for the intended application. Formulationsof compounds of the present invention may be readily administered in avariety of dosage forms such as injectable solutions, topicalpreparations, oral formulations, including sustain-release capsules,hydrogels, colloids, viscous gels, transdermal reagents, intranasal andinhalation formulations, and the like.

The amount, dosage regimen, formulation, and administration of vaccinecompositions disclosed herein will be within the purview of theordinary-skilled artisan having benefit of the present teaching. It islikely, however, that the administration of a diagnostically-effective(i.e., a pharmaceutically-effective) amount of one or more of thedisclosed mRNA-based vaccine compositions may be achieved by a singleadministration, such as, without limitation, a single injection of asufficient quantity of the delivered agent to provide the desiredbenefit to the patient in need thereof. Alternatively, in somecircumstances, it may be desirable to provide multiple, or successiveadministrations of the disclosed compositions, either over a relativelyshort, or even a relatively prolonged period, as may be determined bythe medical practitioner overseeing the administration of suchcompositions to the selected individual undergoing such procedure(s).

Typically, formulations of one or more of the polymeric polyplexcore/phospholipid bilayer shell-based vaccine delivery systems describedherein will contain at least an effective amount of a first activeagent. Preferably, the formulation may contain at least about 0.001% ofeach active ingredient, preferably at least about 0.01% of the activeingredient, although the percentage of the active ingredient(s) may, ofcourse, be varied, and may conveniently be present in amounts from about0.01 to about 90 weight % or volume %, or from about 0.1 to about 80weight % or volume %, or more preferably, from about 0.2 to about 60weight % or volume %, based upon the total formulation. Naturally, theamount of active compound(s) in each composition may be prepared in sucha way that a suitable dosage will be obtained in any given unit dose ofthe compound. Factors such as solubility, bioavailability, biologicalti/2, route of administration, product shelf life, as well as otherpharmacological considerations will be contemplated by one of ordinaryskill in the art of preparing such pharmaceutical formulations, and assuch, a variety of dosages and treatment regimens may be desirable. Inpreferred embodiments, the active agent is an mRNA vaccine componentcomprised within the inner polyplex.

While systemic administration is contemplated to be effective in manyembodiments of the invention, it is also contemplated that formulationsdisclosed herein be suitable for direct injection into one or moreorgans, tissues, or cell types in the body. Direct administration of thedisclosed compositions to particular discreet locations within the body,or directly to tumor or cancerous tissues, e.g., may be conducted usingsuitable means as known to those of ordinary skill in the relevantmedical oncology arts.

The pharmaceutical formulations of the present invention may furthercomprise one or more excipients, buffers, or diluents that areparticularly formulated for contact with mammalian cells, and inparticular human cells, and/or for administration to a mammaliansubject, such as a human patient. Compositions may further optionallycomprise one or more diagnostic or prognostic agents, and/or may beformulated within a population of microspheres, microparticles,nanospheres, or nanoparticles, and may be formulated for administrationto one or more cells, tissues, organs, or body of a human in particular.

Formulation of pharmaceutically-acceptable excipients and carriersolutions is well-known to those of skill in the art, as is thedevelopment of suitable dosing, diagnostic, and/or treatment regimensfor using the particular compositions described herein in a variety ofmodalities, including e.g., without limitation, oral, parenteral,intravenous, intranasal, intratumoral, and intramuscular routes ofadministration.

The particular amount of compositions employed, and the particular timeof administration, or dosage regimen for compositions employing thedisclosed vaccine formulations will be within the purview of a person ofordinary skill in the art having benefit of the present teaching. It islikely, however, that the administration of the disclosed formulationsmay be achieved by administration of one or more doses of theformulation, during a time effective to provide the desired benefit tothe patient undergoing such treatment. Such dosing regimens may bedetermined by the medical practitioner overseeing the administration ofthe compounds, depending upon the particular condition or the patient,the extent or duration of the therapy being administered, etc.

Pharmaceutical formulations comprising one or more active ingredients asdisclosed herein are not in any way limited to use only in humans, oreven to primates, or mammals. In certain embodiments, the methods andcompositions disclosed herein may be employed using avian, amphibian,reptilian, or other animal species. In preferred embodiments, however,the compositions of the present invention are preferably formulated foradministration to a mammal, and in particular, to humans, in a varietyof regimens for modulating the metastatic potential of cancer cells. Asnoted above, such compositions are not limited only to use in humans,but may also be formulated for veterinary administration, including,without limitation, to selected livestock, exotic or domesticatedanimals, companion animals (including pets and such like), non-humanprimates, as well as zoological or otherwise captive specimens, and suchlike.

Compositions for the Preparation of Medicaments

Another important aspect of the present invention concerns methods forusing the disclosed compositions (as well as formulations includingthem) in the preparation of medicaments for preventing, diagnosing,treating and/or ameliorating one or more symptoms of one or morediseases, dysfunctions, abnormal conditions, or disorders in an animal,including, for example, vertebrate mammals. Use of the disclosedcompositions is particularly contemplated in the diagnosis and/orprognosis of cancer, in the detection or prediction of cancer metastasisor in monitoring the extent thereof, and/or for suppression of themetastatic potential of one or more cancer cell types.

Such use generally involves administration to the mammal in need thereofone or more of the disclosed vaccine compositions, in an amount and fora time sufficient to diagnose, treat, lessen, or ameliorate one or moresymptoms of cancer in an affected mammal.

Pharmaceutical formulations including one or more of the disclosedmRNA-based vaccine compositions also form part of the present invention,and particularly those compositions that further include at least afirst pharmaceutically-acceptable excipient for use in the therapyand/or amelioration of one or more symptoms of cancer in an affectedmammal.

Exemplary Definitions

In accordance with the present invention, polynucleotides, nucleic acidsegments, nucleic acid sequences, and the like, include, but are notlimited to, DNAs (including and not limited to genomic or extragenomicDNAs), genes, peptide nucleic acids (PNAs) RNAs (including, but notlimited to, rRNAs, mRNAs and tRNAs), nucleosides, and suitable nucleicacid segments either obtained from natural sources, chemicallysynthesized, modified, or otherwise prepared or synthesized in whole orin part by the hand of man.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. The following referencesprovide one of skill with a general definition of many of the terms usedin this invention: Dictionary of Biochemistry and Molecular Biology,(2^(nd) Ed.) J. Stenesh (Ed.), Wiley-Interscience (1989); Dictionary ofMicrobiology and Molecular Biology (3^(rd) Ed.), P. Singleton and D.Sainsbury (Eds.), Wiley-Interscience (2007); Chambers Dictionary ofScience and Technology (2^(nd) Ed.), P. Walker (Ed.), Chambers (2007);Glossary of Genetics (5^(th) Ed.), R. Rieger et al. (Eds.),Springer-Verlag (1991); and The HarperCollins Dictionary of Biology, W.G. Hale and J. P. Margham, (Eds.), HarperCollins (1991).

Although any methods and compositions similar or equivalent to thosedescribed herein can be used in the practice or testing of the presentinvention, the preferred methods, and compositions are described herein.For purposes of the present invention, the following terms are definedbelow for sake of clarity and ease of reference:

In accordance with long standing patent law convention, the words “a”and “an,” when used in this application, including the claims, denote“one or more.”

The terms “about” and “approximately” as used herein, areinterchangeable, and should generally be understood to refer to a rangeof numbers around a given number, as well as to all numbers in a recitedrange of numbers (e.g., “about 5 to 15” means “about 5 to about 15”unless otherwise stated). Moreover, all numerical ranges herein shouldbe understood to include each whole integer within the range.

As used herein, an “antigenic polypeptide” or an “immunogenicpolypeptide” is a polypeptide which, when introduced into a vertebrate,reacts with the vertebrate's immune system molecules, i.e., isantigenic, and/or induces an immune response in the vertebrate, i.e., isimmunogenic.

“Biocompatible” refers to a material that, when exposed to living cells,will support an appropriate cellular activity of the cells withoutcausing an undesirable effect in the cells, such as a change in a livingcycle of the cells, a change in a proliferation rate of the cells, or acytotoxic effect.

The term “biologically-functional equivalent” is well understood in theart, and is further defined in detail herein. Accordingly, sequencesthat have about 85% to about 90%; or more preferably, about 91% to about95%; or even more preferably, about 96% to about 99%; of nucleotidesthat are identical or functionally-equivalent to one or more of thenucleotide sequences provided herein are particularly contemplated to beuseful in the practice of the methods and compositions set forth in theinstant application.

As used herein, the term “buffer” includes one or more compositions, oraqueous solutions thereof, that resist fluctuation in the pH when anacid or an alkali is added to the solution or composition that includesthe buffer. This resistance to pH change is due to the bufferingproperties of such solutions, and may be a function of one or morespecific compounds included in the composition. Thus, solutions or othercompositions exhibiting buffering activity are referred to as buffers orbuffer solutions. Buffers generally do not have an unlimited ability tomaintain the pH of a solution or composition; rather, they are typicallyable to maintain the pH within certain ranges, for example from a pH ofabout 5 to 7.

As used herein, the term “carrier” is intended to include anysolvent(s), dispersion medium, coating(s), diluent(s), buffer(s),isotonic agent(s), solution(s), suspension(s), colloid(s), inert (s), orsuch like, or a combination thereof that is pharmaceutically acceptablefor administration to the relevant animal or acceptable for atherapeutic or diagnostic purpose, as applicable.

As used herein, the term “DNA segment” refers to a DNA molecule that hasbeen isolated free of total genomic DNA of a particular species.Therefore, a DNA segment obtained from a biological sample using one ofthe compositions disclosed herein refers to one or more DNA segmentsthat have been isolated away from, or purified free from, total genomicDNA of the particular species from which they are obtained. Includedwithin the term “DNA segment,” are DNA segments and smaller fragments ofsuch segments, as well as recombinant vectors, including, for example,plasmids, cosmids, phage, viruses, and the like.

The term “effective amount,” as used herein, refers to an amount that iscapable of treating or ameliorating a disease or condition or otherwisecapable of producing an intended therapeutic effect.

As used herein, the term “epitope” refers to that portion of a givenimmunogenic substance that is the target of, i.e., is bound by, anantibody or cell-surface receptor of a host immune system that hasmounted an immune response to the given immunogenic substance asdetermined by any method known in the art. Further, an epitope may bedefined as a portion of an immunogenic substance that elicits anantibody response or induces a T-cell response in an animal, asdetermined by any method available in the art (see, for example, Geysenet al., 1984). An epitope can be a portion of any immunogenic substance,such as a protein, polynucleotide, polysaccharide, an organic orinorganic chemical, or any combination thereof. The term “epitope” mayalso be used interchangeably with “antigenic determinant” or “antigenicdeterminant site.”

The term “for example” or “e.g.,” as used herein, is used merely by wayof example, without limitation intended, and should not be construed asreferring only those items explicitly enumerated in the specification.

As used herein, a “heterologous” is defined in relation to apredetermined referenced nucleic acid sequence. For example, withrespect to a structural gene sequence, a heterologous promoter isdefined as a promoter which does not naturally occur adjacent to thereferenced structural gene, but which is positioned by laboratorymanipulation. Likewise, a heterologous gene or nucleic acid segment isdefined as a gene or segment that does not naturally occur adjacent tothe referenced promoter and/or enhancer elements.

As used herein, “homologous” means, when referring to polynucleotides,sequences that have the same essential nucleotide sequence, despitearising from different origins. Typically, homologous nucleic acidsequences are derived from closely related genes or organisms possessingone or more substantially similar genomic sequences. By contrast, an“analogous” polynucleotide is one that shares the same function with apolynucleotide from a different species or organism, but may have asignificantly different primary nucleotide sequence that encodes one ormore proteins or polypeptides that accomplish similar functions orpossess similar biological activity. Analogous polynucleotides may oftenbe derived from two or more organisms that are not closely related(e.g., either genetically or phylogenetically).

As used herein, the term “homology” refers to a degree ofcomplementarity between two or more polynucleotide or polypeptidesequences. The word “identity” may substitute for the word “homology”when a first nucleic acid or amino acid sequence has the exact sameprimary sequence as a second nucleic acid or amino acid sequence.Sequence homology and sequence identity can be determined by analyzingtwo or more sequences using algorithms and computer programs known inthe art. Such methods may be used to assess whether a given sequence isidentical or homologous to another selected sequence.

The terms “identical” or percent “identity,” in the context of two ormore nucleic acid or polypeptide sequences, refer to two or moresequences or subsequences that are the same or have a specifiedpercentage of amino acid residues or nucleotides that are the same, whencompared and aligned for maximum correspondence, as measured using oneof the sequence comparison algorithms described below (or otheralgorithms available to persons of ordinary skill) or by visualinspection.

As used herein, the phrase “in need of treatment” refers to a judgmentmade by a caregiver such as a physician or veterinarian that a patientrequires (or will benefit in one or more ways) from treatment. Suchjudgment may made based on a variety of factors that are in the realm ofa caregiver's expertise, and may include the knowledge that the patientis ill as the result of a disease state that is treatable by one or morecompound or pharmaceutical compositions such as those set forth herein.

The phrases “isolated” or “biologically pure” refer to material that issubstantially, or essentially, free from components that normallyaccompany the material as it is found in its native state. Thus,isolated polynucleotides or polypeptides in accordance with the presentdisclosure preferably do not contain materials normally associated withthose polynucleotides or polypeptides in their natural, or in situ,environment.

As used herein, the term “kit” may be used to describe variations of theportable, self-contained enclosure that includes at least one set ofreagents, components, or pharmaceutically-formulated compositions of thepresent invention. Optionally, such kit may include one or more sets ofinstructions for use of the enclosed compositions, such as, for example,in a laboratory or clinical application.

“Link” or “join” refers to any method known in the art for functionallyconnecting one or more proteins, peptides, nucleic acids, orpolynucleotides, including, without limitation, recombinant fusion,covalent bonding, disulfide bonding, ionic bonding, hydrogen bonding,electrostatic bonding, and the like.

The term “naturally-occurring” as used herein as applied to an objectrefers to the fact that an object can be found in nature. For example, apolypeptide or polynucleotide sequence that is present in an organism(including viruses) that can be isolated from a source in nature andwhich has not been intentionally modified by the hand of man in alaboratory is naturally-occurring. As used herein, laboratory strains ofrodents that may have been selectively bred according to classicalgenetics are considered naturally-occurring animals.

As used herein, the term “nucleic acid” includes one or more types of:polydeoxyribonucleotides (containing 2-deoxy-D-ribose),polyribonucleotides (containing D-ribose), and any other type ofpolynucleotide that is an N-glycoside of a purine or pyrimidine base, ormodified purine or pyrimidine bases (including abasic sites). The term“nucleic acid,” as used herein, also includes polymers ofribonucleosides or deoxyribonucleosides that are covalently bonded,typically by phosphodiester linkages between subunits, but in some casesby phosphorothioates, methylphosphonates, and the like. “Nucleic acids”include single- and double-stranded DNA, as well as single- anddouble-stranded RNA. Exemplary nucleic acids include, withoutlimitation, gDNA; hnRNA; mRNA; rRNA, tRNA, micro RNA (miRNA), smallinterfering RNA (siRNA), small nucleolar RNA (snORNA), small nuclear RNA(snRNA), and small temporal RNA (stRNA), and the like, and anycombination thereof.

The term “operably linked,” as used herein, refers to that the nucleicacid sequences being linked are typically contiguous, or substantiallycontiguous, and, where necessary to join two protein coding regions,contiguous and in reading frame. However, since enhancers generallyfunction when separated from the promoter by several kilobases andintronic sequences may be of variable lengths, some polynucleotideelements may be operably linked but not contiguous.

As used herein, the term “patient” (also interchangeably referred to as“recipient” “host” or “subject”) refers to any host that can serve as arecipient for one or more of the vascular access devices as discussedherein. In certain aspects, the recipient will be a vertebrate animal,which is intended to denote any animal species (and preferably, amammalian species such as a human being). In certain embodiments, a“patient” refers to any animal host, including but not limited to, humanand non-human primates, avians, reptiles, amphibians, bovines, canines,caprines, cavines, corvines, epines, equines, felines, hircines,lapines, leporines, lupines, murines, ovines, porcines, racines,vulpines, and the like, including, without limitation, domesticatedlivestock, herding or migratory animals or birds, exotics or zoologicalspecimens, as well as companion animals, pets, and any animal under thecare of a veterinary practitioner.

The phrase “pharmaceutically-acceptable” refers to molecular entitiesand compositions that do not produce an allergic or similar untowardreaction when administered to a human, and in particular, whenadministered to the human eye. The preparation of an aqueous compositionthat contains a protein as an active ingredient is well understood inthe art. Typically, such compositions are prepared as injectables,either as liquid solutions or as suspensions. Alternatively, they may beprepared in solid form suitable for solution or suspension in liquidprior to injection.

As used herein, “pharmaceutically-acceptable salt” refers to a salt thatretains the desired biological activity of the parent compound and doesnot impart any undesired toxicological effects. Examples of such saltsinclude, but are not limited to, acid-addition salts formed withinorganic acids, for example, hydrochloric acid, hydrobromic acid,sulfuric acid, phosphoric acid, nitric acid, and the like; and saltsformed with organic acids such as, for example, acetic acid, oxalicacid, tartaric acid, succinic acid, maleic acid, fumaric acid, gluconicacid, citric acid, malic acid, ascorbic acid, benzoic acid, tannic acid,pamoic (embonic) acid, alginic acid, naphthoic acid, polyglutamic acid,naphthalenesulfonic acids, naphthalenedisulfonic acids, polygalacturonicacid; salts with polyvalent metal cations such as zinc, calcium,bismuth, barium, magnesium, aluminum, copper, cobalt, nickel, cadmium,and the like; salts formed with an organic cation formed fromN,N′-dibenzylethylenediamine or ethylenediamine; and combinationsthereof.

As used herein, the term “plasmid” or “vector” refers to a geneticconstruct that is composed of genetic material (i.e., nucleic acids).Typically, a plasmid or a vector contains an origin of replication thatis functional in bacterial host cells, e.g., Escherichia coli, andselectable markers for detecting bacterial host cells including theplasmid. Plasmids and vectors of the present invention may include oneor more genetic elements as described herein arranged such that aninserted coding sequence can be transcribed and translated in a suitableexpression cells. In addition, the plasmid or vector may include one ormore nucleic acid segments, genes, promoters, enhancers, activators,multiple cloning regions, or any combination thereof, including segmentsthat are obtained from or derived from one or more natural and/orartificial sources.

As used herein, the term “polypeptide” is intended to encompass asingular “polypeptide” as well as plural “polypeptides,” and includesany chain or chains of two or more amino acids. Thus, as used herein,terms including, but not limited to “peptide,” “dipeptide,”“tripeptide,” “protein,” “enzyme,” “amino acid chain,” and “contiguousamino acid sequence” are all encompassed within the definition of a“polypeptide,” and the term “polypeptide” can be used instead of, orinterchangeably with, any of these terms. The term further includespolypeptides that have undergone one or more post-translationalmodification(s), including for example, but not limited to,glycosylation, acetylation, phosphorylation, amidation, derivatization,proteolytic cleavage, post-translation processing, or modification byinclusion of one or more non-naturally occurring amino acids.Conventional nomenclature exists in the art for polynucleotide andpolypeptide structures.

For example, one-letter and three-letter abbreviations are widelyemployed to describe amino acids: Alanine (A; Ala), Arginine (R; Arg),Asparagine (N; Asn), Aspartic Acid (D; Asp), Cysteine (C; Cys),Glutamine (Q; Gln), Glutamic Acid (E; Glu), Glycine (G; Gly), Histidine(H; His), Isoleucine (I; Ile), Leucine (L; Leu), Methionine (M; Met),Phenylalanine (F; Phe), Proline (P; Pro), Serine (S; Ser), Threonine (T;Thr), Tryptophan (W; Trp), Tyrosine (Y; Tyr), Valine (V; Val), andLysine (K; Lys). Amino acid residues described herein are preferred tobe in the “l” isomeric form. However, residues in the “d” isomeric formmay be substituted for l-amino acid residues provided the desiredproperties of the polypeptide be retained.

As used herein, the terms “prevent,” “preventing,” “prevention,”“suppress,” “suppressing,” and “suppression” as used herein refer toadministering a compound either alone or as contained in apharmaceutical composition prior to the onset of clinical symptoms of adisease state so as to prevent any symptom, aspect or characteristic ofthe disease state. Such preventing and suppressing need not be absoluteto be deemed medically useful.

“Protein” is used herein interchangeably with “peptide” and“polypeptide,” and includes both peptides and polypeptides producedsynthetically, recombinantly, or in vitro and peptides and polypeptidesexpressed in vivo after nucleic acid sequences are administered into ahost animal or human subject. The term “polypeptide” is preferablyintended to refer to any amino acid chain length, including those ofshort peptides from about two to about 20 amino acid residues in length,oligopeptides from about 10 to about 100 amino acid residues in length,and longer polypeptides including from about 100 amino acid residues ormore in length. Furthermore, the term is also intended to includeenzymes, i.e., functional biomolecules including at least one amino acidpolymer. Polypeptides and proteins of the present invention also includepolypeptides and proteins that are or have beenpost-translationally-modified, and include any sugar or otherderivative(s) or conjugate(s) added to the backbone amino acid chain.

“Purified,” as used herein, means separated from many other compounds orentities. A compound or entity may be partially purified, substantiallypurified, or pure. A compound or entity is considered pure when it isremoved from substantially all other compounds or entities, i.e., ispreferably at least about 90%, more preferably at least about 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, or greater than 99% pure. A partiallyor substantially purified compound or entity may be removed from atleast 50%, at least 60%, at least 70%, or at least 80% of the materialwith which it is naturally found, e.g., cellular material such ascellular proteins and/or nucleic acids.

The term “recombinant” indicates that the material (e.g., apolynucleotide or a polypeptide) has been artificially or synthetically(non-naturally) altered by human intervention. The alteration can beperformed on the material within or removed from, its naturalenvironment, or native state. Specifically, e.g., a promoter sequence is“recombinant” when it is produced by the expression of a nucleic acidsegment engineered by the hand of man. For example, a “recombinantnucleic acid” is one that is made by recombining nucleic acids, e.g.,during cloning, DNA shuffling or other procedures, or by chemical orother mutagenesis; a “recombinant polypeptide” or “recombinant protein”is a polypeptide or protein which is produced by expression of arecombinant nucleic acid; and a “recombinant virus,” e.g., a recombinantAAV virus, is produced by the expression of a recombinant nucleic acid.

The term “regulatory element,” as used herein, refers to a region orregions of a nucleic acid sequence that regulates transcription.Exemplary regulatory elements include, but are not limited to,enhancers, post-transcriptional elements, transcriptional controlsequences, and such like.

The term “RNA segment” refers to an RNA molecule that has been isolatedfree of total cellular RNA of a particular species. Therefore, RNAsegments can refer to one or more RNA segments (either of native orsynthetic origin) that have been isolated away from, or purified freefrom, other RNAs. Included within the term “RNA segment,” are RNAsegments and smaller fragments of such segments.

The term “sequence,” when referring to amino acids, relates to all or aportion of the linear N-terminal to C-terminal order of amino acidswithin a given amino acid chain, e.g., polypeptide or protein;“subsequence” means any consecutive stretch of amino acids within asequence, e.g., at least 3 consecutive amino acids within a givenprotein or polypeptide sequence. With reference to nucleotide chains,“sequence” and “subsequence” have similar meanings relating to the 5′ to3′ order of nucleotides.

The term “a sequence essentially as set forth in SEQ ID NO:X” means thatthe sequence substantially corresponds to a portion of SEQ ID NO:X andhas relatively few nucleotides (or amino acids in the case ofpolypeptide sequences) that are not identical to, or a biologicallyfunctional equivalent of, the nucleotides (or amino acids) of SEQ IDNO:X. The term “biologically functional equivalent” is well understoodin the art, and is further defined in detail herein. Accordingly,sequences that have about 85% to about 90%; or more preferably, about91% to about 95%; or even more preferably, about 96% to about 99%; ofnucleotides that are identical or functionally equivalent to one or moreof the nucleotide sequences provided herein are particularlycontemplated to be useful in the practice of the invention.

Suitable standard hybridization conditions for nucleic acids for use inthe present invention include, for example, hybridization in 50%formamide, 5×Denhardt's solution, 5×SSC, 25 mM sodium phosphate, 0.1%SDS and 100 μg/mL of denatured salmon sperm DNA at 42° C. for 16 hrfollowed by 1 hr sequential washes with 0.1×SSC, 0.1% SDS solution at60° C. to remove the desired amount of background signal. Lowerstringency hybridization conditions for the present invention include,for example, hybridization in 35% formamide, 5×Denhardt's solution,5×SSC, 25 mM sodium phosphate, 0.1% SDS and 100 μg/mL denatured salmonsperm DNA or E. coli DNA at 42° C. for 16 hr followed by sequentialwashes with 0.8×SSC, 0.1% SDS at 55° C. Those of ordinary skill in theart will recognize that such hybridization conditions can be readilyadjusted to obtain the desired level of stringency for a particularapplication.

As used herein, the term “structural gene” is intended to generallydescribe a polynucleotide, such as a gene, that is expressed to producean encoded peptide, polypeptide, protein, ribozyme, catalytic RNAmolecule, or antisense molecule.

The term “subject,” as used herein, describes an organism, includingmammals such as primates, to which treatment with the compositionsaccording to the present invention can be provided. Mammalian speciesthat can benefit from the disclosed methods of treatment include, butare not limited to, apes; chimpanzees; orangutans; humans; monkeys;domesticated animals such as dogs and cats; livestock such as horses,cattle, pigs, sheep, goats, and chickens; and other animals such asmice, rats, guinea pigs, and hamsters.

The term “substantially complementary,” when used to define either aminoacid or nucleic acid sequences, means that a particular subjectsequence, for example, an oligonucleotide sequence, is substantiallycomplementary to all or a portion of the selected sequence, and thuswill specifically bind to a portion of an mRNA encoding the selectedsequence. As such, typically the sequences will be highly complementaryto the mRNA “target” sequence, and will have no more than about 1, about2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, orabout 10 or so base mismatches throughout the complementary portion ofthe sequence. In many instances, it may be desirable for the sequencesto be exact matches, i.e., be completely complementary to the sequenceto which the oligonucleotide specifically binds, and therefore have zeromismatches along the complementary stretch. As such, highlycomplementary sequences will typically bind quite specifically to thetarget sequence region of the mRNA and will therefore be highlyefficient in reducing, and/or even inhibiting the translation of thetarget mRNA sequence into polypeptide product.

Substantially complementary nucleic acid sequences will be greater thanabout 80 percent complementary (or “% exact-match”) to a correspondingnucleic acid target sequence to which the nucleic acid specificallybinds, and will, more preferably be greater than about 85 percentcomplementary to the corresponding target sequence to which the nucleicacid specifically binds. In certain aspects, as described above, it willbe desirable to have even more substantially complementary nucleic acidsequences for use in the practice of the invention, and in suchinstances, the nucleic acid sequences will be greater than about 90percent complementary to the corresponding target sequence to which thenucleic acid specifically binds, and may in certain embodiments begreater than about 95 percent complementary to the corresponding targetsequence to which the nucleic acid specifically binds, and even up toand including about 96%, about 97%, about 98%, about 99%, and even about100% exact match complementary to all or a portion of the targetsequence to which the designed nucleic acid specifically binds.

Percent similarity or percent complementary of any of the disclosednucleic acid sequences may be determined, for example, by comparingsequence information using the GAP computer program, version 6.0,available from the University of Wisconsin Genetics Computer Group(UWGCG). The GAP program utilizes the alignment method of Needleman andWunsch (1970). Briefly, the GAP program defines similarity as the numberof aligned symbols (i.e., nucleotides or amino acids) that are similar,divided by the total number of symbols in the shorter of the twosequences. The preferred default parameters for the GAP program include:(1) a unary comparison matrix (containing a value of 1 for identitiesand 0 for non-identities) for nucleotides, and the weighted comparisonmatrix of Gribskov and Burgess (1986), (2) a penalty of 3.0 for each gapand an additional 0.10 penalty for each symbol in each gap; and (3) nopenalty for end gaps.

Naturally, the present invention also encompasses nucleic acid segmentsthat are complementary, essentially complementary, and/or substantiallycomplementary to at least one or more of the specific nucleotidesequences specifically set forth herein. Nucleic acid sequences that are“complementary” are those that are capable of base-pairing according tothe standard Watson-Crick complementarity rules. As used herein, theterm “complementary sequences” means nucleic acid sequences that aresubstantially complementary, as may be assessed by the same nucleotidecomparison set forth above, or as defined as being capable ofhybridizing to one or more of the specific nucleic acid segmentsdisclosed herein under relatively stringent conditions such as thosedescribed immediately above.

As used herein, the term “substantially free” or “essentially free” inconnection with the amount of a component preferably refers to acomposition that contains less than about 10 weight percent, preferablyless than about 5 weight percent, and more preferably less than about 1weight percent of a compound. In preferred embodiments, these termsrefer to less than about 0.5 weight percent, less than about 0.1 weightpercent, or less than about 0.01 weight percent.

Probes and primers for use in the present invention may be of anysuitable length. By assigning numeric values to a sequence, for example,the first residue is 1, the second residue is 2, etc., an algorithmdefining all probes or primers contained within a given sequence can beproposed:

n to n+y, where n is an integer from 1 to the last number of thesequence and y is the length of the probe or primer minus one, where n+ydoes not exceed the last number of the sequence. Thus, for a 25-basepairprobe or primer (i.e., a “25-mer”), the collection of probes or primerscorrespond to bases 1 to 25, bases 2 to 26, bases 3 to 27, bases 4 to28, and so on over the entire length of the sequence. Similarly, for a35-basepair probe or primer (i.e., a “35-mer), exemplary primer or probesequence include, without limitation, sequences corresponding to bases 1to 35, bases 2 to 36, bases 3 to 37, bases 4 to 38, and so on over theentire length of the sequence. Likewise, for 40-mers, such probes orprimers may correspond to the nucleotides from the first basepair to bp40, from the second bp of the sequence to bp 41, from the third bp to bp42, and so forth, while for 50-mers, such probes or primers maycorrespond to a nucleotide sequence extending from bp 1 to bp 50, frombp 2 to bp 51, from bp 3 to bp 52, from bp 4 to bp 53, and so forth.

The terms “substantially corresponds to,” “substantially homologous,” or“substantial identity,” as used herein, denote a characteristic of anucleic acid or an amino acid sequence, wherein a selected nucleic acidor amino acid sequence has at least about 70 or about 75 percentsequence identity as compared to a selected reference nucleic acid oramino acid sequence. More typically, the selected sequence and thereference sequence will have at least about 76, 77, 78, 79, 80, 81, 82,83, 84 or even 85 percent sequence identity, and more preferably, atleast about 86, 87, 88, 89, 90, 91, 92, 93, 94, or 95 percent sequenceidentity. More preferably still, highly homologous sequences often sharegreater than at least about 96, 97, 98, or 99 percent sequence identitybetween the selected sequence and the reference sequence to which it wascompared.

As used herein, “synthetic” shall mean that the material is not of ahuman or animal origin.

The term “therapeutically-practical period” means the period of timethat is necessary for one or more active agents to be therapeuticallyeffective. The term “therapeutically-effective” refers to reduction inseverity and/or frequency of one or more symptoms, elimination of one ormore symptoms and/or underlying cause, prevention of the occurrence ofsymptoms and/or their underlying cause, and the improvement or aremediation of damage.

A “therapeutic agent” may be any physiologically or pharmacologicallyactive substance that may produce a desired biological effect in atargeted site in a subject. The therapeutic agent may be achemotherapeutic agent, an immunosuppressive agent, a cytokine, acytotoxic agent, a nucleolytic compound, a radioactive isotope, areceptor, and a pro-drug activating enzyme, which may benaturally-occurring, or produced by synthetic or recombinant methods, orany combination thereof. Drugs that are affected by classical multidrugresistance, such as vinca alkaloids (e.g., vinblastine and vincristine),the anthracyclines (e.g., doxorubicin and daunorubicin), RNAtranscription inhibitors (e.g., actinomycin-D) and microtubulestabilizing drugs (e.g., paclitaxel) may have particular utility as thetherapeutic agent. Cytokines may be also used as the therapeutic agent.Examples of such cytokines are lymphokines, monokines, and traditionalpolypeptide hormones. A cancer chemotherapy agent may be a preferredtherapeutic agent. For a more detailed description of anticancer agentsand other therapeutic agents, those skilled in the art are referred toany number of instructive manuals including, but not limited to, thePhysician's Desk Reference and to Goodman and Gilman's “PharmacologicalBasis of Therapeutics” tenth edition, Hardman et al. (Eds.) (2001).

As used herein, a “transcription factor recognition site” and a“transcription factor binding site” refer to a polynucleotidesequence(s) or sequence motif(s), which are identified as being sitesfor the sequence-specific interaction of one or more transcriptionfactors, frequently taking the form of direct protein-DNA binding.Typically, transcription factor binding sites can be identified by DNAfootprinting, gel mobility shift assays, and the like, and/or can bepredicted based on known consensus sequence motifs, or by other methodsknown to those of ordinary skill in the art.

“Transcriptional regulatory element” refers to a polynucleotide sequencethat activates transcription alone or in combination with one or moreother nucleic acid sequences. A transcriptional regulatory element can,for example, comprise one or more promoters, one or more responseelements, one or more negative regulatory elements, and/or one or moreenhancers.

“Transcriptional unit” refers to a polynucleotide sequence thatcomprises at least a first structural gene operably linked to at least afirst cis-acting promoter sequence and optionally linked operably to oneor more other cis-acting nucleic acid sequences necessary for efficienttranscription of the structural gene sequences, and at least a firstdistal regulatory element as may be required for the appropriatetissue-specific and developmental transcription of the structural genesequence operably positioned under the control of the promoter and/orenhancer elements, as well as any additional cis-sequences that arenecessary for efficient transcription and translation (e.g.,polyadenylation site(s), mRNA stability controlling sequence(s), etc.

As used herein, the term “transformation” is intended to generallydescribe a process of introducing an exogenous polynucleotide sequence(e.g., a viral vector, a plasmid, or a recombinant DNA or RNA molecule)into a host cell or protoplast in which the exogenous polynucleotide isincorporated into at least a first chromosome or is capable ofautonomous replication within the transformed host cell. Transfection,electroporation, and “naked” nucleic acid uptake all represent examplesof techniques used to transform a host cell with one or morepolynucleotides.

As used herein, the term “transformed cell” is intended to mean a hostcell whose nucleic acid complement has been altered by the introductionof one or more exogenous polynucleotides into that cell.

“Treating” or “treatment of” as used herein, refers to providing anytype of medical or surgical management to a subject. Treating caninclude, but is not limited to, administering a composition comprising atherapeutic agent to a subject. “Treating” includes any administrationor application of a compound or composition of the invention to asubject for purposes such as curing, reversing, alleviating, reducingthe severity of, inhibiting the progression of, or reducing thelikelihood of a disease, disorder, or condition or one or more symptomsor manifestations of a disease, disorder, or condition. In certainaspects, the compositions of the present invention may also beadministered prophylactically, i.e., before development of any symptomor manifestation of the condition, where such prophylaxis is warranted.Typically, in such cases, the subject will be one that has beendiagnosed for being “at risk” of developing such a disease or disorder,either as a result of familial history, medical record, or thecompletion of one or more diagnostic or prognostic tests indicative of apropensity for subsequently developing such a disease or disorder.

The term “vector,” as used herein, refers to a nucleic acid molecule(typically comprised of DNA) capable of replication in a host celland/or to which another nucleic acid segment can be operatively linkedso as to bring about replication of the attached segment. A plasmid,cosmid, or a virus is an exemplary vector.

The expressions “zero-order” or “near-zero-order” as applied to therelease kinetics of active agents from the disclosed vaccine deliverycompositions is intended to include a rate of release of the activeagent in a controlled manner over a therapeutically practical timeperiod following administration of the composition, such that atherapeutically effective plasma concentration of the active agent isachieved.

In certain embodiments, it will be advantageous to employ one or morenucleic acid segments of the present invention in combination with anappropriate detectable marker (i.e., a “label,”), such as in the case ofemploying labeled polynucleotide probes in determining the presence of agiven target sequence in a hybridization assay. A wide variety ofappropriate indicator compounds and compositions are known in the artfor labeling oligonucleotide probes, including, without limitation,fluorescent, radioactive, enzymatic or other ligands, such asavidin/biotin, etc., which are capable of being detected in a suitableassay. In particular embodiments, one may also employ one or morefluorescent labels or an enzyme tag such as urease, alkaline phosphataseor peroxidase, instead of radioactive or other environmentallyless-desirable reagents. In the case of enzyme tags, colorimetric,chromogenic, or fluorogenic indicator substrates are known that can beemployed to provide a method for detecting the sample that is visible tothe human eye, or by analytical methods such as scintigraphy,fluorimetry, spectrophotometry, and the like, to identify specifichybridization with samples containing one or more complementary orsubstantially complementary nucleic acid sequences. In the case ofso-called “multiplexing” assays, where two or more labeled probes aredetected either simultaneously or sequentially, it may be desirable tolabel a first oligonucleotide probe with a first label having a firstdetection property or parameter (for example, an emission and/orexcitation spectral maximum), which also labeled a secondoligonucleotide probe with a second label having a second detectionproperty or parameter that is different (i.e., discreet or discerniblefrom the first label. The use of multiplexing assays, particularly inthe context of genetic amplification/detection protocols are well-knownto those of ordinary skill in the molecular genetic arts.

Biological Functional Equivalents

Modification and changes may be made in the structure of the nucleicacids, or to the vectors comprising them, as well as to mRNAs,polypeptides, or therapeutic agents encoded by them and still obtainfunctional vaccine delivery systems that contain one or more therapeuticagents with desirable characteristics. As mentioned above, it is oftendesirable to introduce one or more mutations into a specificpolynucleotide sequence. In certain circumstances, the resulting encodedpolypeptide sequence is altered by this mutation, or in other cases, thesequence of the polypeptide is unchanged by one or more mutations in theencoding polynucleotide.

When it is desirable to alter the amino acid sequence of a polypeptideto create an equivalent, or even an improved, second-generationmolecule, the amino acid changes may be achieved by changing one or moreof the codons of the encoding DNA sequence, according to Table 1.

For example, certain amino acids may be substituted for other aminoacids in a protein structure without appreciable loss of interactivebinding capacity with structures such as, for example, antigen-bindingregions of antibodies or binding sites on substrate molecules. Since itis the interactive capacity and nature of a protein that defines thatprotein's biological functional activity, certain amino acid sequencesubstitutions can be made in a protein sequence, and, of course, itsunderlying DNA coding sequence, and nevertheless obtain a protein withlike properties. It is thus contemplated by the inventors that variouschanges may be made in the peptide sequences of the disclosedcompositions or corresponding DNA sequences which encode said peptideswithout appreciable loss of their biological utility or activity.

TABLE 1 AMINO ACIDS CODONS Alanine Ala A GCA GCC GCG GCU Cysteine Cys CUGC UGU  Aspartic acid Asp D GAC GAU  Glutamic acid Glu E GAA GAG Phenylalanine Phe F UUC UUU  Glycine Gly G GGA GGC GGG GGU Histidine HisH CAC CAU  Isoleucine Ile I AUA AUC AUU Lysine Lys K AAA AAG  LeucineLeu L UUA UUG CUA CUC CUG CUU Methionine Met M AUG  Asparagine Asn NAAC AAU  Proline Pro P CCA CCC CCG CCU Glutamine Gln Q CAA CAG  ArginineArg R AGA AGG CGA CGC CGG CGU Serine Ser S AGC AGU UCA UCC UCG UCUThreonine Thr T ACA ACC ACG ACU Valine Val V GUA GUC GUG GUU TryptophanTrp W UGG  Tyrosine Tyr Y UAC UAU 

In making such changes, the hydropathic index of amino acids may beconsidered. The importance of the hydropathic amino acid index inconferring interactive biologic function on a protein is generallyunderstood in the art (Kyte and Doolittle, 1982, incorporate herein byreference). It is accepted that the relative hydropathic character ofthe amino acid contributes to the secondary structure of the resultantprotein, which in turn defines the interaction of the protein with othermolecules, for example, enzymes, substrates, receptors, DNA, antibodies,antigens, and the like. Each amino acid has been assigned a hydropathicindex based on its hydrophobicity and charge characteristics (Kyte andDoolittle, 1982). These values are: isoleucine (+4.5); valine (+4.2);leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5);methionine (+1.9); alanine (+1.8); glycine (−0.4); threonine (−0.7);serine (−0.8); tryptophan (−0.9); tyrosine (−1.3); proline (−1.6);histidine (−3.2); glutamate (−3.5); glutamine (−3.5); aspartate (−3.5);asparagine (−3.5); lysine (−3.9); and arginine (−4.5).

It is known in the art that certain amino acids may be substituted byother amino acids having a similar hydropathic index or score and stillresult in a protein with similar biological activity, i.e. still obtaina biological functionally equivalent protein. In making such changes,the substitution of amino acids whose hydropathic indices are within ±2is preferred, those within ±1 are particularly preferred, and thosewithin ±0.5 are even more particularly preferred. It is also understoodin the art that the substitution of like amino acids can be madeeffectively based on hydrophilicity. U.S. Pat. No. 4,554,101(specifically incorporated herein in its entirety by express referencethereto), states that the greatest local average hydrophilicity of aprotein, as governed by the hydrophilicity of its adjacent amino acids,correlates with a biological property of the protein.

As detailed in U.S. Pat. No. 4,554,101, the following hydrophilicityvalues have been assigned to amino acid residues: arginine (+3.0);lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3);asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (−0.4);proline (−0.5±1); alanine (−0.5); histidine (−0.5); cysteine (−1.0);methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8);tyrosine (−2.3); phenylalanine (−2.5); tryptophan (−3.4). It isunderstood that an amino acid can be substituted for another having asimilar hydrophilicity value and still obtain a biologically equivalent,and in particular, an immunologically equivalent protein. In suchchanges, the substitution of amino acids whose hydrophilicity values arewithin ±2 is preferred, those within ±1 are particularly preferred, andthose within ±0.5 are even more particularly preferred.

As outlined above, amino acid substitutions are generally thereforebased on the relative similarity of the amino acid side-chainsubstituents, for example, their hydrophobicity, hydrophilicity, charge,size, and the like. Exemplary substitutions that take one or more of theforegoing characteristics into consideration are well known to those ofordinary skill in the art, and include arginine and lysine; glutamateand aspartate; serine and threonine; glutamine and asparagine; andvaline, leucine and isoleucine.

The section headings used throughout are for organizational purposesonly and are not to be construed as limiting the subject matterdescribed. All documents, or portions of documents, cited in thisapplication (including, but not limited to, patents, patentapplications, articles, books, and treatises) are expressly incorporatedherein in their entirety by express reference thereto. In the event thatone or more of the incorporated literature and similar materials definesa term in a manner that contradicts the definition of that term in thisapplication, this application controls.

EXAMPLES

The following examples are included to demonstrate illustrativeembodiments of the invention. It should be appreciated by those ofordinary skill in the art that the techniques disclosed in theseexamples represent techniques discovered to function well in thepractice of the invention, and thus can be considered to constitutepreferred modes for its practice. However, those of ordinary skill inthe art should, in light of the present disclosure, appreciate that manychanges can be made in the specific embodiments that are disclosed, andstill obtain a like or similar result without departing from the spiritand scope of the invention.

Example 1—Lipopolyplex Potentiates Anti-Tumoral Immunity of mRNA-BasedVaccines

In this example, a lipopolyplex mRNA vaccine is described, whichconsists of a poly-(β-amino ester) polymer mRNA core encapsulated into a1,2-dioleoyl-sn-glycero-3-ethylphosphocholine/1,2-dioleoyl-sn-glycero-3-phosphatidyl-ethanolamine/1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethyleneglycol)-2000(EDOPC/DOPE/DSPE-PEG) lipid shell. This core-shell structured mRNAvaccine enters dendritic cells through macropinocytosis. It displayedintrinsic adjuvant activity by potently stimulating interferon-α andinterleukin-12 expression in dendritic cells through Toll-like receptor7/8 signaling. Dendritic cells treated with the mRNA vaccine displayedenhanced antigen presentation capability. Mice bearing lung metastaticB16-OVA tumors expressing the ovalbumin antigen were treated with thelipopolyplex mRNA, and over 90% reduction of tumor nodules was observed.Collectively, this core-shell structure provides an excellent system fordelivery of mRNA vaccines to mammalian cells.

FIG. 1A schematically illustrates the synthesis of an exemplaryshell/core-mRNA lipopolyplex vaccine composition in accordance with oneaspect of the invention. In the shell/core-mRNA vaccine,negatively-charged mRNA was condensed inside a positively-chargedpolymer, which together formed a tight polyplex “core” structure thatwas a few nanometers to a few hundred nanometers in diameter. Thispolyplex core was then encapsulated by a hydrophilic, phospholipidbilayer “shell” that both enhanced uptake by dendritic cells, andprotected the mRNA molecules within the inner core from being degradedby cellular nucleases. The resulting three-component shell/core/mRNAcomposition could also be further modified by loading one or moresoluble adjuvants into space between the polyplex-mRNA inner core andthe outer lipid shell, to further enhance anti-tumoral immunity.

The results described herein reveal multiple advantages of the disclosedshell/core-mRNA-polyplex-structured vaccine system, as compared toconventional compressed core-mRNA vaccines. Encapsulating the polyplexcore-mRNA particles into a phospholipid outer shell not only protectedthe core mRNA molecules from degradation, but it also significantlyimproved uptake of the vaccine particles by antigen-presenting dendriticcells (FIG. 1A). Additionally, the presence of a lipid shell structureencapsulating the core prohibited the core-mRNA molecules frominteracting with non-DC immune cells, which limited potentialundesirable side effects. Furthermore, the LPP-mRNA vaccine compositionsdisclosed herein were more potent than conventional “naked” mRNA-corevaccines in stimulating expression of IFN-α and IL-12 (cytokines thatplay an important role in mediating anti-tumor immunity throughpromoting DC maturation) (FIG. 4A). Moreover, the LPP-mRNA vaccines werevery potent in mediating tumor cell killing. Finally, theshell/core/mRNA multi-component vaccine compositions described hereinalso provided an effective option for encapsulate soluble adjuvants orother stimulatory molecules in the lipid shell whenever there is a needto further enhance the activity of antigen-presenting cells. All ofthese properties highlight the utility of this therapeutic vaccineplatform in the creation of new immunotherapeutic agents in therapidly-evolving era of precision medicine.

Materials and Methods

Synthesis of Poly-(β-Amino Ester) Polymer (PbAE).

The PbAE (MW˜4 kDa) was synthesized in a two-step reaction procedure aspreviously described (Kamat et al., 2013). In the first step, the basepolymer was synthesized by mixing 1,4-butanediol diacrylate(Sigma-Aldrich) with 5-amino-1-pentanol (Sigma-Aldrich) at a molar ratioof 1.2:1. The reaction was maintained at 90° C. for 24 hrs in a glassscintillating vial with a teflon stir bar. The base polymer was dried,and then dissolved in anhydrous dimethyl sulfoxide (DMSO) at a finalconcentration of 167 mg/mL. In the second step, 480 μL of the basepolymer solution was mixed with 320 μL of 0.5 mol/L (PEO)4-bis-amine(Molecular Biosciences, Boulder, Colo., USA) in a 1.5-mL Eppendorf tube,and the reaction was allowed for 24 hrs at room temperature. The polymermix was first dialyzed against milli-Q water in a dialysis tube (MWCO3,500 Da) to remove the bulk of free reagents, and then mixed with 4×the volume of ethyl ether (Sigma-Aldrich) and vortexed vigorouslyfollowed by centrifugation at 4,000 rpm for 5 min to further removeunreacted monomers in the supernatant. The purified polymers werevacuum-dried and then dissolved in 25 mM sodium acetate, pH 5.2.

Preparation of PbAE/mRNA Polyplex.

PbAE/mRNA polyplex was prepared by mixing one volume of the PbAE polymerwith two volumes of mRNA molecules (Trilink Biotechnologies, San Diego,Calif., USA). After incubation for 20 min at 20° C., the polyplex wasanalyzed for size distribution and zeta potential using a MalvernZetasizer Nano ZS dynamic light scattering instrument (MalvernInstruments, Inc., Worcestershire, UNITED KINGDOM). The PbAE/mRNApolyplex was also analyzed in a gel retardation assay. Briefly, apolyplex sample containing 250 ng mRNA was loaded into each well andseparated by electrophoresis in a 0.7% agarose gel with 1×TBE buffer(BioRad, Hercules, Calif., USA). RNA bands were stained with Gelrednucleic acid gel stain (Biotium, Hayward, Calif., USA) and visualizedwith a GelDoc system (BioRad, Hercules, Calif., USA).

Preparation and Characterization of LPP/mRNA Vaccines.

The lipids 1,2-dioleoyl-sn-glycero-3-ethylphosphocholine (EDOPC),1,2-dioleoyl-sn-glycero-3-phosphatidyl-ethanolamine (DOPE),1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethyleneglycol)-2000 (DSPE-PEG-2000), cholesteryl hemi succinate (CHEMS) and1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) were purchased fromAvanti Polar Lipids (Birmingham, Ala., USA). Cholesterol was obtainedfrom Sigma-Aldrich (St. Louis, Mo., USA). The reagents were dissolved inchloroform at a final concentration of 20 mg/mL and applied to preparethin lipid films by rotary evaporation in a Buchi Rotavapor (Oldham,UNITED KINGDOM) under partial vacuum. The thin lipid film was composedof 49% EDOPC, 49% DOPE and 2% DSPE-PEG. The lipid film was rehydratedwith a solution containing PbAE/mRNA polyplex to prepare thelipopolyplex mRNA vaccine. Size distribution and zeta potential of theLPP/mRNA vaccine were measured with DLS and transmission electronicmicroscopy (TEM). The same procedure was applied to prepareCHEMS/DOPE/octaarginine (CHEMS/DOPE/R8) andDOTAP/Cholesterol/DSPE-PEG-2000 (DOTAP/Chol/DSPE-PEG-2000)lipopoly-plexes. To prepare protamine/mRNA polyplex, protamine sulfate(grade X, Sigma Aldrich) was mixed with mRNA at weight ratio of 2:1 in10 mM Tris-HCL buffer, followed by a 30-min incubation at roomtemperature.

Cellular Uptake of LPP/mRNA Vaccine In Vitro.

Immortalized DC2.4 (a murine bone marrow-derived dendritic cell line)cells were applied to test protein expression from the LPP/mRNA vaccine.Briefly, cells were seeded in a 24-well plate at a seeding density of1.5×10⁵ cells/well, and maintained in 1 mL RPMI-1640 complete medium(supplemented with 10% fetal bovine serum [FBS, Atlas Biological, FortCollins, Colo., USA], 1% penicillin/streptomycin [10,000 unitspenicillin and 10 mg streptomycin, Sigma-Aldrich] and 0.1%β-mercaptoethanol [Sigma-Aldrich]). Cells were incubated with LPPpackaged with 0.5 μg eGFP mRNA (LPP/eGFP mRNA) for 24 hrs, and eGFPexpression was visualized using an Eclipse TE2000-S fluorescencemicroscope (Nikon Corporation, Tokyo, JAPAN). Flow cytometry wasperformed to measure percentage of GFP-positive cells using an Accuri C6flow cytometer (Becton Dickinson, Franklin Lakes, N.J., USA). The sameprocedure was also applied to determine eGFP expression in humanMDA-MB-231 breast cancer cells (American Type Culture Collection;Manassas, Va., USA) and murine mDMEC skin endothelial cells after theywere incubated with LPP/eGFP mRNA, respectively.

To determine route of cellular internalization of the LPP/mRNA vaccine,DC2.4 cells were seeded at a density of 1.5×10⁵ cells/well in a 24-wellplate and incubated for 24 hrs at 37° C. They were then treated withFAM-labeled mRNA packaged in LPP (LPP/FAM-mRNA) and one of the followingsmall molecule inhibitors: amiloride (0.2 mM), chloroquine (100 mM),genistein (50 chlorpromazine (15 or pimozide (10 Cells were allowed togrow for 4 hrs before they were washed with ice-cold PBS and applied todetermine particle uptake via fluorescence microscopy.

Cytotoxicity from LPP/mRNA In Vitro.

To test potential cytotoxicity from LPP/mRNA vaccine, DC2.4, MDA-MB-231and endothelial cells were seeded in a 96-well plate at a seedingdensity of 3×10⁴ cells/well, and treated with LPP/0.1 μg mRNA. Cellviability was measured 24 hrs later with a tetrazolium-based CellTiter96® Aqueous One Solution Cell Proliferation (MTS) assay (Promega, Inc.,Madison, Wis., USA) following the manufacturer's instructions.

Preparation of Bone Marrow-Derived Dendritic Cells (BMDCs).

BMDCs were prepared from C57BL/6 mice as previously described (Xia etal., 2015). Briefly, bone marrow cells from the femur and tibia wereflushed out with 2% FBS-containing phosphate buffer saline (PBS) using asyringe. Cells were centrifuged at 500×g for 4 min, treated with ACKlysis buffer (Lonza, Inc.) to remove red blood cells, and resuspended inRPMI-1640 culture medium supplemented with 10% FBS, 0.5%β-mercaptoethanol, 1% penicillin/streptomycin, 20 ng/mLgranulocyte-macrophage colony-stimulating factor (GM-CSF), and 20 ng/mLinterleukin-4 (IL-4). They were seeded into 6-well plates at a seedingdensity of 1×10⁶ cells/mL, and growth medium was changed every otherday. The non-adherent dendritic cells were harvested on Day 5.

Measurement of Pro-Inflammatory Cytokines.

BMDCs were seeded at a density of 3×10⁵ cells/well in a 24-well plate,and treated with LPP/0.5 μg OVA mRNA. Disassembled components of theLPP/mRNA vaccine (the liposome shell and the polyplex core) served asnegative controls. After 24 hrs of incubation, supernatants werecollected, and IL-6, TNF-α, IFN-β and IL-12 concentrations were measuredwith an ELISA kit for cytokine measurement (eBioscience, San Diego,Calif., USA).

TLR7/8 Inhibition.

DC2.4 cells were seeded in a 24-well plate at a density of 1.5×10⁵cells/1 mL RPMI-1640 complete medium, and incubated for 24 hrs at 37° C.Cells were then treated with the TLR7/8 inhibitor ODN 2087 (MilitenlyBiotec, San Diego, Calif., USA) at a final concentration of 2.5 μM for 1hr at 37° C. Subsequently, LPP/0.5 μg OVA mRNA was added into theculture, and cell growth was maintained for another 24 hrs before cellculture medium was collected for cytokine analysis. Dendritic cellswithout TLR inhibitor treatment served as the positive control, andcells without LPP/OVA mRNA treatment were used as the negative control.

Evaluation of Dendritic Cell Maturation.

DC2.4 cells were seeded in 24-well plates at a density of 1.5×10⁵cells/well supplied with 1 mL RPMI complete medium. They were treatedwith LPP/0.5 μg mRNA and incubated at 37° C. for 24 hrs. Cells were thenwashed with PBS, stained with antibodies specific for CD11c, CD40, CD86and MHC II (BD Bioscience), and applied for flow cytometry analysis witha BD Accuri C6 flow cytometer (Becton Dickinson, Inc., Franklin Lakes,N.J., USA).

MHC I and II-Restricted Antigen Presentation Assays.

To measure antigen presentation, BMDCs treated with LPP/OVA mRNA werestained for 10 min at room temperature with a pentamer that recognizesthe OVA257-264-H-2Kb complex (H-2Kb/SIINFEKL, BD Bioscience, San Jose,Calif., USA). Cells were then stained for 30 min with an anti-CD11cantibody (BD Bioscience) and analyzed using an Accuri C6 flow cytometer.

To determine T cell activation, BMDC and DC2.4 cells were treated withLPP/0.5 μg OVA mRNA for 24 hrs. Cells were washed with PBS andco-cultured either with B3Z OVA-specific CD8 T cells or DOBWOVA-specific CD4 T cells at a DC/T cell ratio of 1:1. ELISA wasperformed to measure IL-2 secretion by the activated T cells. Allsamples were measured in triplicate.

In Vitro Killing of B16-OVA Melanoma Cells by Cytotoxic T Cell.

DC2.4 were seeded at a density of 1.5×10⁵ cells/well in a 24-well plate.After overnight incubation, cells were treated with LPP/0.5 μg OVA mRNAfor 24 hrs at 37° C. These DC2.4 cells were subsequently co-culturedwith B3Z T cells at a DC2.4/T cell ratio of 1:2. After 24 hrs'incubation, the activated T cells were applied to co-culture with B16melanoma cells at T cell/tumor cell ratio of 5:1 for 4, 8 or 24 hrs at37° C. Tumor cell viability was then determined using a MTS formazanviability assay (Promega, Inc., Madison, Wis., USA) as described above.Tumor cells treated with non-activated T cells or with T cells activatedwith a HER2 breast cancer antigen peptide served as negative controls.All samples were measured in triplicate.

Efficacy Test in Murine Model of Lung Metastatic Melanoma.

Eight-week-old male and female C57BL/6 mice were inoculated with 2.5×10⁵B16-OVA melanoma tumor cells by tail vein injection to establish lungmetastatic tumors following a previously described protocol (Overwijkand Restifo, 2001). Three days after tumor inoculation, mice weresubcutaneously vaccinated with LPP/OVA mRNA (1 μg). Vaccination wasboosted at Days 7 and 10 with two more inoculations. Mice wereeuthanized on Day 18, and lungs were harvested and fixed with 4%paraformaldehyde. Number of lung metastatic tumor nodules was countedunder a dissecting microscope.

Bioluminescence Imaging in Live Mice.

BALB/c mice were administered subcutaneously with 10 μg of luciferasemRNA loaded into LPP (LPP/Luc mRNA). Mice were injectedintraperitoneally with 30 μg RediJect D-luciferin Ultra (Perkin-Elmer)24 or 48 hrs later, and bioluminescence was measured in a XenogenIVIS-200 imaging system.

Efficacy Test in Murine Model of Lung Metastatic Melanoma.

Eight-week-old male and female C57BL/6 mice were inoculated with 2.5×10⁵B16-OVA melanoma tumor cells by tail vein injection to establish lungmetastatic tumors. Three days after tumor inoculation, mice weresubcutaneously vaccinated with LPP/OVA mRNA (1 mg). Vaccination wasboosted at days 7 and 10 with two more inoculations. Mice wereeuthanized on day 18, and lungs were harvested and fixed with 4%paraformaldehyde. Number of lung metastatic tumor nodules was countedunder a dissecting microscope.

In Vivo T Cell Activation Analysis.

To determine T cell activation status, C57BL/6 mice were immunized s.c.with 2.5 mg LPP/OVA mRNA. To determine T cell activation by surfacemarker, mice were euthanized 24 hrs later, and spleen and lymph nodeswere collected, processed, and stained with an anti-murine CD3, CD4, CD8or CD69 antibody (Ebioscience) for 30 min at 4° C., and then analyzed byflow cytometry using BD Accuri C6 flow cytometer (BD Bioscience, SanJose, Calif., USA). To measure T cell activation by IFN-γ secretion,C57BL/6 mice were immunized s.c. with LPP/OVA mRNA or LPP/TRP2 mRNA onDays 1, 4 and 7. One week after the last immunization, spleen, lymphnodes, and PBMCs were collected and processed for single cell analysis.Cells were re-stimulated with OT-I (OVA257-264), OT-II (OVA323-339), orPMA-Ionomycin for 48 hrs at 37° C. IFN-γ secretion was analyzed by ELISA(eBioscience).

Statistical Analysis.

Two-tailed Student's t-test was applied for comparison betweenexperimental groups. P<0.05 was considered statistically significant.

Results

Lipopolyplex-Based mRNA Vaccine is Optimal for Dendritic Cell Uptake andProtein Expression.

A platform is described for mRNA-based vaccines that include a PbAE/mRNApolyplex core structure packaged into a lipid bilayer envelope (FIG.1A). Agarose gel electrophoresis was performed to examine mRNA bindingcapacity to the cationic PbAE polymer, and it was determined that mRNAwas fully encapsulated into PbAE when PbAE/mRNA ratio (wt./wt.) was 20or beyond (FIG. 1B). Consequently, a PbAE/mRNA ratio of 20 was chosen toprepare LPP mRNA vaccines in the rest of the study. TEM analysisdetected a 50-nm PbAE/mRNA polyplex core (FIG. 1C) surrounded by anEDOPC/DOPE/DSPE-PEG-2000 lipid shell (FIG. 1D, FIG. 1E, and FIG. 1F).

Lipid shell for the LPP/mRNA vaccine was compared amongEDOPC/DOPE/DSPE-PEG-2000, DOTAP/Chol/DSPE-PEG-2000, and CHEMS/DOPE/R8.DOTAP/Chol/DSPE-PEG-2000 forms a cationic lipid shell, and CHEMS/DOPE/R8is a lipid shell with an active targeting moiety; both have previouslybeen applied for RNA delivery (Wang et al., 2013; Hayashi et al., 2015).DC2.4 served as the antigen presenting cells and mRNA molecules encodingthe eGFP protein was applied to prepare the polyplex core. Cellsincubated with the PbAE/mRNA core did not express a detectable level ofeGFP (FIG. 1G). While cells treated with EDOPC/DOPE/DSPE-PEG-2000 andDOTAP/Chol/DSPE-PEG-2000-packaged particles expressed bright eGFPproteins, those incubated with CHEMS/DOPE/R8-packaged polyplex did nothave a detectable level of eGFP (FIG. 1H, FIG. 1I, and FIG. J).Interestingly, cells treated with protamine/eGFP did not have a highlevel of eGFP expression either (FIG. 1K), although the protamine-basedmRNA vaccines are at different stages of clinical trials (Kallen andThess, 2014). In addition, a high level of cytotoxicity was detectedfrom the DOTAP/Chol/DSPE-PEG-2000 formulation (FIG. 1L). Consequently,EDOPC/DOPE/DSPE-PEG-2000 was selected for LPP/mRNA vaccine preparationin all follow-up studies.

LPP/mRNA Vaccine Enters Dendritic Cells Through Macropinocytosis.

Uptake of the LPP/mRNA vaccine particles by different cell types wasinvestigated. An equal amount of EDOPC/DOPE/DSPE-PEG-2000 particlespackaged with PbAE/eGFP mRNA was added into culture of DC 2.4 cells,MDA-MB-231 human breast cancer cells or the mDMEC murine endothelialcells, and cells expressing eGFP were detected 24 hrs later. In linewith the notion that DCs are the most effective antigen-presentationcells with a high phagocytic potential (Banchereau and Steinman, 1998),all DC2.4 cells had internalized the vaccine particles and expressed thegreen fluorescent protein; in comparison, about half number ofMDA-MB-231 cells were GFP-positive, and only a small fraction of theendothelial cells synthesized GFP (FIG. 2).

The mechanism of cellular uptake was examined by treating DC2.4 cellswith inhibitors of endocytosis, macropinocytosis and phagocytosis.Treatment with amiloride, an inhibitor of macropinocytosis (Koivusalo etal., 2010), reduced cellular uptake of theEDOPC/DOPE/DSPE-PEG-2000-packaged, FAM-fluorescent-dye-labeled mRNA(LPP/FAM-mRNA) by 70%. In comparison, cellular uptake of the particleswas not significantly affected by the caveolin-mediated endocytosisinhibitor, genistein; the clathrin-mediated endocytosis inhibitor,chlorpromazine; or the phagocytosis inhibitor, pimozide (see FIG. 3A,FIG. 3B, FIG. 3C, FIG. 3D, FIG. 3E, FIG. 3F, and FIG. 3G).

These result suggested that macropinocytosis was the major route of cellentry for the disclosed LPP mRNA-based vaccines. Significantly,chloroquine, a reagent that prevents endosome acidification andmaturation, did not affect mRNA accumulation (FIG. 3A, FIG. 3B, FIG. 3C,FIG. 3D, FIG. 3E, FIG. 3F, and FIG. 3G). Time-dependent monitoring ofchloroquine-treated cells showed a delayed increase in fluorescenceintensity, with a peak intensity reached 120 min after incubation (FIG.311). This result indicated that the mRNA molecules successfully exitedendosomes and entered the cytosol.

LPP mRNA Vaccine Promotes DC Maturation.

Murine tumor models with an overexpressed ovalbumin (OVA) have beenwidely applied to test the effectiveness of cancer vaccines (Kim et al.,2015; Avci et al., 2011; Uhlig et al., 2015). OVA mRNA was applied toassemble the therapeutic mRNA vaccine (LPP/OVA), and examined anti-tumorimmunity in vitro and in vivo. In an in vitro setting, bonemarrow-derived DCs (BMDCs) were co-incubated either with LPP/OVA orcontrols, and cytokine levels in the cell growth media were measured.Interestingly, both the polyplex/OVA core and LPP/OVA, together withprotamine/OVA, could trigger significant TNF-α expression (FIG. 4A). Ithas been previously reported that TNF-α-dependent DC maturation iscritical for activating the adaptive immune responses to viral infection(Trevejo et al., 2001) and for anti-tumoral immunity (Brunner et al.,2000). However, neither polyplex/OVA nor protamine/OVA was as potent asLPP/OVA in stimulating IFN-β and IL-12 expression (FIG. 4A). It has beenpreviously shown that Type I interferon IFN-β promotes DC maturation,antigen processing and presentation, and stimulation of T cell clonalexpansion (Xia et al., 2015). Likewise, IL-12 is one of the Th1cytokines (Mills and Ley, 2014), and DCs that produce IL-12 promote typeI CD8⁺ T cell immunity (Carreno et al., 2013; Carreno et al., 2015). Theresults indicate that both the polyplex/mRNA core and the lipid shellare needed in order to maximize the adjuvant effect from the vaccine.LPP/mRNA-mediated adjuvant effect was mediated through activation of theTLR-7/8 signaling, in line with the protamine-condensed mRNA particles(Scheel et al., 2005; Fotin-Mleczek et al., 1997), as treatment with theshort single-stranded oligodeoxynucleotide TLR7/8 inhibitor, ODN2087,completely suppressed LPP/OVA-stimulated IL-12 and IFN-β expression(FIG. 4B).

DC maturation markers were also examined in the LPP/OVA-treated DC2.4cells. The post-treatment cells showed a dramatically increased level ofMHC II expression (FIG. 4C). It has been reported that DCs express ahigher level of MHC II loaded with peptides derived from antigens at theplasma membrane upon activation (Trombetta and Mellman, 2005). Inaddition, levels of the other DC maturation markers, CD40 and CD86, werealso higher in the treated cells.

LPP mRNA Vaccine Stimulates Antigen Presentation.

Antigen processing and presentation were analyzed in BMDCS treated withLPP/OVA. Flow cytometry detected CD11c⁺ DCs that also displayed MHCI-OVAepitope on cell surface (FIG. 5A). When the post-treatment cells wereco-incubated with OVA-specific CD4⁺ or CD8⁺ T cells, we detectedsignificant increases in IL-2 secretion by the antigen-specific T cells(FIG. 5B), indicating the DCs had successfully processed and presentedOVA epitopes that could be recognized by the T cells. These resultsdemonstrated that BMDCs could properly translate the mRNA antigen, aswell as process and present the antigen epitopes. In a separate study,similar effects were observed with post-treatment DC2.4 cells (FIG. 5C).

LPP mRNA Vaccine has a Potent Anti-Tumor Activity.

To test tumor cell killing in vitro, activated OVA-specific T cells wereco-cultured with B16-OVA melanoma cells at an effector T cell/tumor cellratio of 5:1, and the time-dependent tumor cell killing was examined. Asignificant decrease in B16-OVA tumor cell viability was observed asearly as 4 hrs after co-incubation, and most tumor cells were dead bythe 24-hr time point (FIG. 6A).

In comparison, tumor cells treated with naïve T cells did not show asignificant cell death. To confirm antigen-specific tumor cell killing,B16-OVA cells were co-incubated with T cells specific for the HER2breast cancer antigen, but not OVA, and no cell death was observed.

Anti-tumor activity was further evaluated in a B16-OVA melanoma lungmetastasis model. Mice were treated with subcutaneous injection ofLPP/OVA three times, and euthanized 8 days after the last treatment toexamine tumor growth in the lung. Mice in the PBS control groupdeveloped extensive pulmonary metastases; in comparison, those treatedwith the LPP/OVA mRNA showed a 96% decrease in number of tumor nodulesin the lung (FIG. 6B), demonstrating the power of the LPP mRNA vaccinein treating metastatic tumors.

In a separate study, C57BL6 mice bearing B16 melanoma were treated withanother mRNA vaccine targeting TRP2 (LPP/TRP2 mRNA). A significant levelof IFN-γ expression by PBMCs was detected in the vaccinated mice. About4% total PBMCs were TRP2-specific CD8k T cells. These resultsdemonstrated that the LPP/mRNA platform is not restricted to just onespecific mRNA, indicting its potential for broad applications in thefight against cancers (see FIG. 7).

Example 2—Lipopolyplex Potentiates Anti-Tumoral Immunity of mRNA-BasedVaccines

FIG. 8A and FIG. 8B show the size distribution of untargeted andtargeted mRNA vaccine particles. The targeted mRNA vaccine has mannoseon the surface of lipid shell. Since dendritic cells express a mannosereceptor and tend to bind to particles with a mannose moiety on surfacewith a high binding affinity. It was prepared by following the sameprocedure as untargeted mRNA vaccine. Lipid composition for the shell is49% EDOPC, 49% DOPE, 1% DSPE-PEG, and 1% DSPE-PEG-mannose. Bothuntargeted and targeted mRNA vaccine particles are within 40-200 nmrange, and medium size of the targeted particles is bigger than theuntargeted ones.

FIG. 12A and FIG. 12B show that dendritic cells take up targeted mRNAvaccine more effectively than untargeted mRNA vaccine. The targeted mRNAvaccine has mannose on the surface of lipid shell. It was prepared byfollowing the same procedure as untargeted mRNA vaccine. Lipidcomposition for the shell is 49% EDOPC, 49% DOPE, 1% DSPE-PEG, and 1%DSPE-PEG-mannose. Cy5 fluorescent dye-labeled mRNA molecules werepackaged into untargeted or targeted vaccines. The vaccines wereincubated with DC2.4 cells (an immortalized dendritic cell line) for 4hrs, and flow cytometry was performed to detect cells that have taken upthe fluorescent vaccine particles. The percentage of DC2.4 cellsinternalized with the fluorescent mRNA vaccine is shown in FIG. 12A,while FIG. 12B shows the total fluorescent intensity in DC2.4 cells.These results indicated that surface conjugation of an affinity moiety(i.e., mannose) is an effective approach to enhance dendritic celluptake of the vaccine particles.

FIG. 17 shows IDO1 inhibitor enhanced antigen presentation by dendriticcells. mRNA vaccines were prepared by encapsulating both OVA mRNA coreand the IDO1 inhibitor INCB024360 inside the lipid shell. mRNA vaccineswith or without INCB024360 were used to treat BMIDCs, and the BMIDCswere then applied to co-incubate with B3Z OVA-specific T cells.Stimulated T cells secreted IL-2 into growth media, and ELISA wasapplied to measure IL-2 level. Based on the result, inclusion of theIDO1 inhibitor could further stimulate T cell activation.

FIG. 18A and FIG. 18B show the anti-tumor immune responses from OVA mRNAvaccine. C57BL6 mice were either treated with OVA protein or OVA mRNAvaccine on days 1, 4 and 7. One week after the last treatment, mice wereeuthanized, and the spleens, lymph nodes and peripheral blood sampleswere collected. (FIG. 18A) Single cells prepared from spleens and lymphnodes were re-stimulated with OTI (OVA₂₅₇₋₂₆₄₀ or OTII (OVA₃₂₃₋₃₃₉)peptides for 48 hours, and ELISA was applied to measure secretedinterferon-γ level in media. (FIG. 18B) T cells from peripheral bloodwere co-incubated with B16-OVA tumor cells, and cell viability wasmeasured 24 hrs later. This result indicates that treatment with OVAmRNA vaccine, but not OVA protein, promotes generation of OVAantigen-specific T cells that are effective in killingantigen-expressing tumor cells.

Example 3—a Generalized Description of the mRNA Vaccine Platform

FIG. 20 illustrates an overall description of the mRNA vaccine platformdisclosed herein. The vaccine is preferably composed of a plurality ofhydrophobic “core” structures (each comprising at least one mRNAencoding an antigen of interest), that are comprised within hydrophilic“shell” structures (comprised of a liposomal-bilayer and formulated toeffectively encapsulate the core structures therein). The hydrophobic“core” preferably includes a population of negatively-charged mRNAmolecules and positively-charged polyplex (e.g., PbAE) or protein (e.g.,protamine) molecules, while the hydrophilic “shell” is preferablycomposed of a combination of lipids and/or phospholipids in apre-selected and optimized ratio. In certain embodiments, it may bedesirable to “functionalize” the surface of the lipid shell byconjugating one or more affinity moieties to it (e.g., sugar moietiessuch as mannose, binding proteins, or antibodies specific for one ormore DC-expressing epitopes) to enhance the interaction and/or increasethe binding between the vaccine particle and the antigen-presentingcells to be targeted (such as dendritic cells, macrophages, and B cells)by the vaccine core/shell complex. The “cytosolic” space formed betweenthe internal core containing the mRNA, and the outer liposomal bilayershell, can also be optimized to contain one or more cytokines (e.g.,CpG), proteins (e.g., FLT3L), or small molecules (e.g., animmunomodulatory agent such as an IDO-1 inhibitor), thereby furtherenhancing/extending the activity of the vaccine in selected cells andpatients.

In preferred embodiments, a ratio of ≥20:1 polymer-to-mRNA molecules (oralternatively, ≥1:1 protamine-to-mRNA molecules) was determined toprovide the most desirable results when preparing the shell/coredelivery constructs for the therapeutic compositions disclosed herein.Likewise, a ratio of approximately 1 μg of mRNA to 2 μg of protamine to20 μg of lipid was shown to be particularly advantageous in formulatingvaccines for human administration.

Example 4—Two mRNAs-can be Co-Packaged in Single Shell for DualImmunotherapy

In the study shown in FIG. 21, 500 ng OVA mRNA was mixed with increasingamounts of mRNA encoding IL12p70 to prepare the protamine/mRNA core,followed by packaging the core into lipid shell. So, the resulting mRNAvaccine contained two different mRNA molecules: mRNA to encode the OVAantigen and mRNA to encode the dendritic cell-stimulating cytokineIL12p70. DC2.4 cells were first treated with the mRNA vaccines, and thenco-incubated with B3Z OVA-specific T cells. IL-2 level in cell growthmedium was measured 24 hrs later. Results showed that co-packaging of500 ng of IL12p70 mRNA boosted vaccine activity. This demonstratedthat 1) it was possible to package two different types of mRNA moleculesin one vaccine particle; and 2) the two types of mRNA molecules couldserve different purposes—one for antigen production, the other fordendritic cell stimulation.

This result demonstrated an important aspect of the present invention,particularly with respect to design of “personalized” cancerimmunotherapies, which are created for specific patients. Thisapplication is farther extended in the studies described in thefollowing example:

Example 5—mRNA-Based Vaccines for Personalized Cancer Immunotherapy

Advances in identification of somatic mutations from a cancer genome andprediction of immunogenic tumor mutations have provided unprecedentedopportunities to develop therapeutic vaccines for personalized cancerimmunotherapy. However, it is a daunting task to prepare the traditionalprotein- or peptide-based vaccines in order to target cancer cells witha heterogeneous mutation spectrum in a given tumor. The disclosed mRNAvaccine platform has been specifically designed for this purpose. Here,this highly-effective platform was used to test the hypothesis thatpersonalized breast cancer treatment could be achieved throughcustomized vaccination based on unique cancer genomic features of thepatients.

This example addresses three major challenges in breast cancer research:

-   -   a) revolutionizing treatment regimens by replacing them with        ones that are more effective, less toxic, and impact survival;    -   b) eliminating the mortality associated with metastatic breast        cancer; and    -   c) determining why and how breast cancer cells lie dormant for        years and then re-emerge, and using this information to prevent        such recurrence.

Cancer immunotherapy has achieved unprecedented clinical efficacy inmultiple types of cancers in recent years. However, only a small numberof cancer patients benefit from immunotherapy, and many patients fail torespond or mount effective antitumor immune responses. Multiple lines ofevidence have shown that the presence of tumor-infiltrating lymphocytes(TIL) serves as a prognostic marker and predicts response to differenttherapies including immunotherapy and chemotherapy. Tumors lacking TILhave been characterized as “non-inflamed,” and generally correlate withtreatment failure and poor prognosis. For example, the efficacy ofcheckpoint blockade antibody in patients with breast cancer patients,which has relatively less TIL is far less effective compared to that inpatients with melanoma or non-small cell lung carcinoma, tumor typeswith abundant TIL that are characterized as “inflamed.” Thus, a meansfor promoting T cell infiltration and maintaining function of T cells inthe tumor microenvironment is a focus for developing effectiveimmunotherapy, especially for the “non-inflamed” tumor types includingbreast cancer.

Therapeutic cancer vaccines have the potential to stimulate potentanti-tumor immunity. In a recent study, a nanotechnology-based dendriticcell vaccine (nano-DC vaccine) containing a p66 HER2 antigen peptide wasutilized to target HER2-positive breast cancer, and detect massive tumorinfiltration of antigen-specific CD8⁺ T cells and stimulation ofTh1-biased cytokines, which resulted in potent inhibition ofHER2-positive tumor growth in a murine model of breast cancer.

A follow-up study also demonstrated synergy between treatment with thecancer vaccine and treatment with an anti-PD-1 antibody in furtherpromoting tumor infiltration of T cells, as demonstrated by increasedCD3⁺ T cells within the tumor-associated CD45⁺ cell population.

Therapeutic mRNA Vaccine in the New Era of Personalized Immunotherapy.

Although the overall mutation load in breast cancer is not as heavy asin melanoma or non-small cell lung cancer, a recent study of 560 breastcancer whole genome sequences identified 1,628 likely driver mutationsin 93 cancer genes, and TP53 was the most commonly mutated driver cancergenes in estrogen receptor (ER)-negative breast cancer. This resultmatches nicely with a previous report that TP53 mutations occur morefrequently in HER2-positive (72%) and basal-like (80%) breast cancers,while PIK3CA mutations are rare in basal-like breast cancers (9%)compared to other subtypes (29-45%). Using online tools that are basedon proteasome cleavage motifs, multiple cytotoxic T cell epitopes havebeen identified that are 100% conserved between the human and murineproteins including those in TP53, PIK3CA and PTEN (Table 2). Theseepitopes serve as the best reagents for development of “next-generation”immunotherapeutics, and the results obtained from efficacy studies usingmurine tumor models can be applied directly to predict patientresponses.

TABLE 2 CYTOTOXIC T CELL EPITOPES IN BC Peptide Name Peptide Sequence*SEQ ID NO: X TP53-170 TEVVRRCPH SEQ ID NO: 1 TP53-170* TEVV H RCPHSEQ ID NO: 2 TP53-258 TLEDSSGN SEQ ID NO: 3 TP53-258* T D EDSSGNSEQ ID NO: 4 PIK3CA-106 GNREEKNRE SEQ ID NO: 5 PIK3CA-106* GNRE N KNRESEQ ID NO: 6 PIK3CA-721 QEKLKDETQK SEQ ID NO: 7 PIK3CA-721* QEKLKD K TQKSEQ ID NO: 8 PTEN-63 NHYKIYNLC SEQ ID NO: 9 PTEN-63* NHY N IYNLCSEQ ID NO: 10 *The amino acid sequences in the wild-type proteins areprovided as reference, and mutant amino acids are underlined.

The mRNA-based vaccine platform disclosed herein has been developedideally for this purpose. Using an LPP mRNA vaccine, which was comprisedof an mRNA core in a liposomal shell structure where the polyplex/mRNAcore is composed of poly-(β-amino ester) polymer/mRNA (PβAE/mRNA) orprotamine/mRNA, and the liposome shell is made of a mixture of neutraland positively charged phospholipids, the platform allows for robustprotein expression from the mRNA molecules. In contrast to conventionalpeptide-based vaccines, mRNA-based vaccines have the advantage toincorporate multiple antigen epitopes in one minigene construct, andthus can be customized quickly to fit the need for individual patientsbased on their mutation spectrum in the individual cancer genome. Theyalso differ from traditional plasmid-derived vaccines in that (amongother advantages), they function in both dividing and non-dividingcells, while there is also no risk for genomic integration.Interestingly, although protamine-based mRNA vaccine products have beentested for many years, protein antigen expression from nakedprotamine/mRNA was only a fraction of LPP/mRNA. A possible reason isthat mRNA molecules in the naked construct are vulnerable to attack byplasma RNases.

Alternatively, LPP/mRNA triggers DCs to express a much higher level ofIL-12, a cytokine that is essential to maximum antigen processing andpresentation activity of the antigen-presentation cells. The mRNA corealso serves as a strong adjuvant for the vaccine by activating theToll-like receptor 7 and 8 (TLR7/8) signaling, as demonstrated by theinhibition of cytokine expression by the TLR7/8 inhibitor ODN2095. Totest activity of the mRNA vaccine, ovalbumin (OVA) was applied as amodel antigen, and bone marrow-derived dendritic cells (BMDCs) wereincubated with LPP/OVA to determine antigen presentation and T cellactivation. BMDCs incubated with LPP/OVA, but not protamine/OVA,displayed a high level of major histocompatibility complex type I(MHCI)-OVA epitope on the surface. Treatment with the LPP/OVA mRNAvaccine caused stimulation of CD4+ and CD8+ T cells in the spleen andlymph nodes. This vaccine was also effective in inhibiting growth ofOVA-expressing tumors. In a separate study, it was shown that thedisclosed LPP/mRNA vaccines were much more effective than simpleliposomal mRNA vaccines (i.e., those lacking the mRNA-protective corestructure) in promoting antigen expression and stimulating DCactivation, despite prominent recent publications on liposomal mRNAvaccines with a similar structure and composition for cancer andinfectious diseases. Taken together, these data showed that the LPP/mRNAvaccine platform provides robust anti-tumor immunity through potentantigen processing and presentation. The polyplex/mRNA core—liposomeshell structure is far superior over other mRNA-based platforms (nakedprotamine/mRNA and liposome-encapsulated mRNA) in stimulating anti-tumorimmunity.

It is well known that human cancers are heterogeneous both in molecularand structural features, and gene mutations/amplifications/deletionsoccurs frequently during tumor growth, clonal expansion, and drugtreatment. Compounding this complexity is that each cancer type has itsown unique features. For example, triple-negative breast cancer (TNBC,lacking expression of the estrogen receptor, progesterone receptor orHER2/neu) has a high rate of TP53 mutation that is combined with lowfrequency mutations in a wide variety of genes. These mutation eventsmost likely will cause formation of different clones (some dominant andsome not well represented) with specific gene amplification/mutationfeatures in a single tumor. Consequently, it is not uncommon to identifydifferent mutation spectra in different tumor nodules from the samepatient or between the primary and metastatic tumors. The goal of cancerimmunotherapy is to eliminate all clones in the tumor with highefficiency, and the mRNA cancer vaccine suits this purpose very well,since one single vaccine construct can be engineered to target multipleantigens to match the complexity of the cancer genome in each patient.

Generation of Primary and Metastatic Tumors in Immune Competent Mice:

4T1 murine mammary gland tumor cells (p53 null) will be engineered togenerate a point mutation in the PIK3CA or PTEN gene with theCRISPR/Cas9 technology, a practice that is routinely performed in thelaboratory. 4T1 cells with wild-type or PIK3CA and PTEN mutations willthen be infected with a retrovirus that carries a mutant TP53 gene and aluciferase gene. The resulting isogenic 4T1 cells will either carry asingle mutation in the TP53 gene (4T1/TP53*), double mutations in theTP53 gene and in PIK3CA or PTEN (4T1/TP53*PIK3CA* or 4T1/TP53*PTEN*), ormutations in all three genes (4T1/TP53*PIK3CA*PTEN*). All four isogeniclines are pooled together at 1:1:1:1 ratio, and inoculated into themammary gland fat pad of 6 to 8-week-old female BALB/c mice to generateprimary tumor. As demonstrated in the previous example, 4T1 primarytumors develop metastases to the liver and lung with a high efficiency.Histological analysis is performed to characterize primary tumors andmetastatic tumor nodules and compared to the parental 4T1 tumors. Singlecells from the tumors may be isolated and quantitated using polymerasechain reactions (PCR) to measure percentage of tumor cells that carry asingle TP53* mutation or double or triple mutations in a given tumor.

Test of Immune Responses In Vitro:

Cell-based studies may be performed to ensure the mRNA vaccines canexert their intended functions before they are applied to treattumor-bearing murine model. Individual mRNA vaccines may be incubatedwith bone marrow-derived dendritic cells (BMDCs) for 6 hrs, and then theBMDCs are co-incubated with murine T cells. DC maturation can bedetermined by flow cytometry analysis on CD40 and CD86 expression and byELISA on interleukin-12 (IL-12) expression. T cell activation ismeasured by interferon (IFN-I) and interleukin-2 (IL-2) expression.

Examination of Immune Responses from mRNA Vaccines In Vivo:

BALB/c mice will be inoculated with 4T1 cells comprising a mixture of 4isogenic clones in the mammary gland fat pads. When the primary tumorsreach 200-300 mm³, mice will be divided into 4 groups (n=10 mice/group)and treated intradermally with the 4 mRNA vaccines, and vaccination willbe boosted one more time a week later. Blood samples will be collectedonce before the second vaccination and another time at the completion ofthe experiment. Mice will be euthanized 3 days after the secondvaccination, and the spleens, lymph nodes, and tumor samples will becollected. All samples will be applied to isolate CD3⁺ T cells using anEasySep™ mouse T cell isolation kit (StemCell Technologies), andactivated cells will be detected based on IL-2 and IFN-I expressionlevel or surface maturation markers or using the ELISPOT assay,following the same protocols as we have described. Expression levels ofthe checkpoint inhibitor proteins will also be examined.

Evaluation of Anti-Tumor Activity from mRNA Vaccines:

BALB/c mice will be inoculated with the parental 4T1 tumors or tumorderived from a mixture of 4 isogenic clones (n=10 mice/group) will bedivided into 4 groups and treated intradermally (i.d.) with the 4 mRNAvaccines weekly for 4 weeks. Mice will be maintained for monitoring oftumor growth (based on tumor size) and tumor metastasis to distantorgans (using a Xenogen IVIS-200 imaging system). Mice will beeuthanized when the weight of primary tumor (calculated based on tumorvolume assuming density as 1 g/cm³) exceeds 10% of body weight, tumorulceration, or signs of sickness including lethargic, hunch back andruffed fur.

Immune Responses to mRNA Vaccines in HLA-A2 Transgenic Mice:

The HLA-A2 transgenic mice from the Jackson Laboratories(C57BL/6-Tg[HAL-A2.1]1Enge/J) express the human HLA-A2.1 MHCI leukocyteantigens on cells from the spleen, bone marrow and thymus. To predictpatient immune responses to the mRNA vaccine, HLA-A2 mice (n=10mice/group) are treated with the four listed mRNA vaccines, and bloodand tissue samples are collected and examined for antigen-specific Tcell activities.

Murine Tumor Model:

Mice inoculated with mixed isogenic clones will develop tumors withmixed molecular features. In case tumor cells from one isogenic clonegrow much faster than the rest clones, which will be detected based onPCR analysis of the tumor samples, the ratio of these clones may beadjusted before tumor cell inoculation. If signals from the primarytumors interfere with detection of metastatic nodules, the primarytumors may be surgically removed when they reach 500 cm³, and tumormetastasis monitored by luminescence assay.

Anti-Tumor Immunity:

Analysis of immune responses reveals that mRNA vaccines can exertpowerful anti-tumor immunity. Vaccines encoding multiple neoantigenepitopes (e.g., LPP/p53-PI3K-PTEN) are expected to have an advantage inpromoting stronger anti-tumor immunity compared to vaccines having asingle epitope (i.e., LPP/p53), and the effect will be reflected by Tcell activity measurement and inhibition of tumor growth and metastasis.If treatment with certain vaccines, such as LPP/p53 or LPP/p53-PI3K,only causes partial inhibition of tumor growth, tumor tissues can becollected from post-vaccinated mice, and tumor composition analyzed,with a focus on percentage of tumor cells from the 4 individual isogenicclones. Changes in tumor composition would indicate efficacy (or lack ofefficacy) from certain vaccine(s). One potential risk with the mRNAvaccines is that the MHCI neoantigen epitopes were chosen based on a setof algorithms, but have not been confirmed with biological studies. Incase no or very weak response would be observed from the selectedepitopes based on results from a particular in vitro study, alternativeepitopes may be utilized in a repeat of the study until a number ofsuccessful candidates are obtained. Alternatively, antigen epitopes maybe modified with single amino acid substitutions to enhance MHC binding,a strategy that has been successfully applied to develop WT1 MHCIantigens.

Study with HLA A2 Mice:

Since peptide sequences that cover the MHCI neoantigen epitope region isconserved between the human protein and the mouse homolog, we expectthat similar immune responses would be observed from BALB/c mice andHLA-A2 transgenic mice.

Therapeutic cancer vaccines must activate antigen-presenting cells,primarily DCs, in order to exert their anti-tumor activities. To fullyunderstand the mechanism of action of mRNA-based therapeutic cancervaccines and to identify approach to further improve activities of thisnovel therapeutic, it is necessary first to identify thesubpopulation(s) of DCs essential to drive anti-tumor immunity. In thisstudy, experiments were selected to determine the role of 3 majorsubsets of DCs in mRNA vaccine activity: the conventional CD8⁺ and CD8″DCs (cDCs) and the plasmacytoid DCs (pDCs). Three genetically-engineeredmouse lines have been obtained from The Jackson Laboratories for thisstudy: Batf.3^(−/−) knockout, zDC-DTR (diphtheria toxin receptor [DTR]in the 3′ untranslated region of the Zbt646 gene), and Cd11c-DTR (DTRunder the control of CD11c promoter). The Batf3^(−/−) knockout mice donot generate CD8⁺ DCs. Treatment of the zDC-DTR mice with diphtheriatoxin (DT) depletes both types of cDCs from the bone marrow, but doesnot affect pDCs, while DT treatment of the Cd11c-DTR mice will depleteall DCs from the body.

Anti-Tumor Immunity in Wild-Type and Genetically Engineered Mice:

To assess the role of CD8⁺ DCs in anti-tumor immunity, 4T1 tumor cellsare inoculated in Batf.3^(−/−) knockout mice in BALB/c background orcontrol wild-type mice (n=10 mice/group), and animals are treated withLPP/p53-PI3K-PTEN mRNA vaccine weekly for 4 weeks. To evaluate theimpact of cDCs and pDCs on mRNA vaccine activity, the tumor-bearingzDC-DTR and Cd11c-DTR mice are divided into 2 treatment groups per line(n=10 mice/group). Mice in the control groups receive no treatment withDT, while those in the treatment groups are dosed with DT (20 μg/kg,i.p.) 24 hrs prior to vaccination. Depletion of the DC subsets isconfirmed by flow cytometry analysis prior to the full-scale efficacystudies. Tumor growth and metastasis is monitored, and mice areeuthanized when they display signs of sickness.

Based on mechanism of action of mRNA vaccines, depletion of all DCs inthe Cd11c-DTR mice should completely eliminate anti-tumor immunity fromthe mRNA vaccine. Results from the Batf3^(−/−) knockout and zDC-DTR miceshould illustrate which DC subset plays an essential role to promotemRNA vaccine activity. In the prior example, strong responses to mRNAvaccine treatment were observed from BMDCs, indicating the involvementof CD8⁺ DCs. If the target subset of DCs is not completely removed inthe zDC-DTR or Cd11c-DTR mice after 20 μg/kg DT treatment (a protocolused by multiple laboratories), DT dosage and/or dosing schedule may beadjusted as needed.

REFERENCES

The following references, to the extent that they provide exemplaryprocedural or other details supplementary to those set forth herein, arespecifically incorporated herein in their entirety by express referencethereto:

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It should be understood that the examples and embodiments describedherein are for illustrative purposes only and that various modificationsor changes in light thereof will be suggested to persons skilled in theart and are to be included within the spirit and purview of thisapplication and the scope of the appended claims.

All references, including publications, patent applications and patents,cited herein are hereby incorporated by reference to the same extent asif each reference was individually and specifically indicated to beincorporated by reference and was set forth in its entirety herein.

Recitation of ranges of values herein are merely intended to serve as ashorthand method of referring individually to each separate valuefalling within the range, unless otherwise indicated herein, and eachseparate value is incorporated into the specification as if it wereindividually recited herein.

The description herein of any aspect or embodiment of the inventionusing terms such as “comprising”, “having”, “including,” or“containing,” with reference to an element or elements is intended toprovide support for a similar aspect or embodiment of the invention that“consists of,” “consists essentially of,” or “substantially comprises,”that particular element or elements, unless otherwise stated or clearlycontradicted by context (e.g., a composition described herein ascomprising a particular element should be understood as also describinga composition that contains and/or that includes that particularelement, unless otherwise explicated stated, or clearly contradicted bycontext).

All of the compositions and methods disclosed and claimed herein can bemade and executed without undue experimentation in light of the presentdisclosure. While the compositions and methods of this invention havebeen described in terms of preferred embodiments, it will be apparent tothose of skill in the art that variations may be applied to thecompositions and methods and in the steps or in the sequence of steps ofthe method described herein without departing from the concept, spiritand scope of the invention. More specifically, it will be apparent thatcertain agents that are chemically- and/or physiologically-related maybe substituted for the agents described herein while the same or similarresults would be achieved. All such similar substitutes andmodifications apparent to those skilled in the art are deemed to bewithin the spirit, scope, and concept of the invention as defined by theappended claims.

What is claimed is:
 1. A composition comprising a population of mRNAmolecules that encode an antigen, wherein the population of mRNAmolecules is comprised within a plurality of polyplex or protein coreparticles comprising at least a polymer or protein, wherein theplurality of polyplex or protein core particles are themselvesencapsulated in a biocompatible lipid bilayer shell, and wherein thebiocompatible lipid bilayer shell comprises: (a) from about 45% to about55% of 1,2-dioleoyl-sn-glycero-3-ethylphosphocholine (EDOPC); (b) fromabout 55% to about 45% of1,2-dioleoyl-sn-glycero-3-phosphatidyl-ethanolamine (DOPE); and (c) fromabout 1% to about 2% of 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethylene glycol)-2000] (DSPE-PEG).
 2. The compositionof claim 1, wherein the biocompatible lipid bilayer shell facilitatesmacropinocytosis of the plurality of polyplex or protein core particlesby one or more mammalian antigen-presenting cells.
 3. The composition ofclaim 1, further comprising an adjuvant selected from the groupconsisting of CpG, poly(I:C), alum, and any combination thereof,encapsulated within the biocompatible lipid bilayer shell.
 4. Thecomposition of claim 1, further comprising an immunomodulatory compoundselected from the group consisting of an IL-12p70 protein, a FLT3ligand, and an indoleamine 2,3-dioxygenase (IDO-1) inhibitor, whereinthe immunomodulatory compound is encapsulated within the space insidethe biocompatible lipid bilayer shell.
 5. The composition of claim 4,wherein the IDO-1 inhibitor is GDC-0919, INCB24360, or a combinationthereof.
 6. The composition of claim 1, wherein the polymer or proteincomprises protamine, polyethyleneimine, poly-(B-amino ester), or anycombination thereof.
 7. The composition of claim 1, wherein the antigenis specific to a mammalian cell.
 8. The composition of claim 7, whereinthe population of mRNA molecules encode at least one cancer- ortumor-specific protein, polypeptide or peptide, or an antigenic fragmentthereof.
 9. The composition of claim 8, wherein the population of mRNAmolecules encodes at least one human tumor-specific protein, polypeptideor peptide selected from the group consisting of HER2p66, HER2E75,HER2^(YVMA) TRP2, p66, and any combination thereof.
 10. The compositionof claim 1, further comprising a therapeutic agent selected from thegroup consisting of an immunomodulating agent, an antineoplastic agent,a cytotoxic agent, a cytostatic agent, a neuroactive agent, ananti-inflammatory agent, an anti-lipidemic agent, a hormone, a receptoragonist, a receptor antagonist, an anti-infective agent, a protein, apeptide, an antibody, an antigen-binding fragment, an enzyme, an RNA, aDNA, an siRNA, an mRNA, a ribozyme, a hormone, a cofactor, a steroid, anantisense molecule, and any combination thereof.
 11. The composition ofclaim 10, wherein the therapeutic agent is selected from the groupconsisting of cyclophosphamide, doxorubicin, 5-fluorouracil, docetaxel,paclitaxel, trastuzumab, methotrexate, epirubicin, cisplatin,carboplatin, vinorelbine, capecitabine, gemcitabine, mitoxantrone,isabepilone, eribulin, lapatinib, carmustine, a nitrogen mustard, asulfur mustard, a platin tetranitrate, vinblastine, etoposide,camptothecin, and any combination thereof.
 12. The composition of claim1, further comprising an antigenic polypeptide, an antigenic fusionpolypeptide, an antigenic peptide, or an antigenic fragment thereof. 13.The composition of claim 1, comprised within a population of mesoporoussilicon particles, nanoparticles, microparticles, or any combinationthereof.
 14. The composition of claim 1, further comprising one or moresurfactants, liposomes, niosomes, ethosomes, transferosomes,phospholipids, sphingosomes, or any combination thereof.
 15. Thecomposition of claim 1, further comprising one or morepharmaceutically-acceptable carriers, buffers, diluents, vehicles, orexcipients.
 16. The composition of claim 1, formulated for systemic,intradermal or intravenous administration to a mammal.
 17. Thecomposition of claim 1, comprised within an isolated population ofmammalian antigen-presenting cells comprising macrophage cells, B cells,dendritic cells, or any combination thereof.
 18. The composition ofclaim 1, adapted and configured as part of a therapeutic kit thatcomprises the composition, and at least a set of instructions foradministration of the composition to a human in need thereof.
 19. Anisolated population of mammalian cells comprising the composition ofclaim
 1. 20. The isolated population of mammalian cells of claim 19,wherein the mammalian cells are selected from the group consisting ofdendritic cells, macrophages, B cells, and any combination thereof. 21.A kit comprising: 1) the composition of claims 1; and 2) instructionsfor administering the composition to a mammal in need thereof, as partof a regimen for the prevention, treatment, or amelioration of one ormore symptoms of a disease, a disorder, or a dysfunction in the mammal.22. A method of treating or ameliorating one or more symptoms of acancer disease or infectious disease in a mammal in need thereof, themethod comprising administering to the mammal an effective amount of acomposition for a time sufficient to treat or ameliorate the one or moresymptoms of the disease, disorder, or dysfunction in the mammal, whereinthe composition comprises a population of mRNA molecules that encode anantigen, wherein the population of mRNA molecules is comprised within aplurality of polyplex or protein core particles comprising at least apolymer or protein, wherein the plurality of polyplex or protein coreparticles are themselves encapsulated in a biocompatible lipid bilayershell, and wherein the biocompatible lipid bilayer shell comprises: (a)from about 45% to about 55% of EDOPC; (b) from about 55% to about 45% ofDOPE; and (c) from about 1% to about 2% of DSPE-PEG.
 23. The method ofclaim 22, wherein the disease is diagnosed as, or is identified as, arefractory, a metastatic, a relapsed, or a treatment-resistant cancer.24. The method of claim 23, wherein the cancer is metastatic breastcancer, metastatic lung cancer, or metastatic melanoma.
 25. The methodof claim 22, wherein the mammal is human.
 26. The method of claim 22,wherein the method further comprises administering atherapeutically-effective amount of radiation or an additionalchemotherapeutic to the mammal.
 27. The method of claim 22, wherein thecomposition is administered systemically to the mammal, in a singleadministration, or in a series of multiple administrations over a periodof one or more days, over a period of one or more weeks, or over aperiod of one or more months or longer.
 28. The method of claim 22,wherein the composition further comprises a chemotherapeutic agent, or atherapeutic cancer vaccine.
 29. A method of administering an mRNA thatencodes an antigen to a population of cells within the body of amammalian subject in need thereof, comprising administering to thesubject an effective amount of a composition, wherein the compositioncomprises a population of mRNA molecules that encode an antigen, whereinthe population of mRNA molecules is comprised within a plurality ofpolyplex or protein core particles comprising at least a polymer orprotein, wherein the plurality of polyplex or protein core particles arethemselves encapsulated in a biocompatible lipid bilayer shell, andwherein the biocompatible lipid bilayer shell comprises: (a) from about45% to about 55% of EDOPC; (b) from about 55% to about 45% of DOPE; and(c) from about 1% to about 2% of DSPE-PEG.
 30. The composition of claim1, wherein the polymer or protein is positively-charged.